id string | task_type string | pipeline string | difficulty string | num_hops int64 | question string | context string | reasoning_chain dict | answer string | choices list | modalities list | modality_data list | evidence list | metadata unknown | path_confidence_score float64 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
co_coun_00009 | counterfactual | coding_variant | hard | 3 | If MLH1 were knocked out, the BASC complex (BRCA1-associated genome surveillance complex) complex would lose one of its members, indirectly affecting ATM, another member of the same complex. Which disease association of ATM could therefore be indirectly affected? | MLH1 PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-associated genome surveillance complex) -> ATM PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-associated genome surveillance complex) -> ATM GENE_ASSOCIATED_WITH_DISEASE digestive system neoplasm | {
"steps": [
{
"hop": 1,
"source_node_id": "MLH1",
"source_node_type": "GENE",
"source_node_label": "MLH1",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "CO... | digestive system neoplasm | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MLH1",
"source_db": "UniProt",
"payload": {
"accession": "P40692",
"sequence": "MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGK... | [
{
"source_db": "OmniPath",
"source_id": "CORUM:433",
"text": "MLH1 PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-associated genome surveillance complex)",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "ATM",
"text": "ATM PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-asso... | {
"knocked_out_gene": "MLH1",
"disrupted_complex": "BASC complex (BRCA1-associated genome surveillance complex)",
"complex_partner": "ATM",
"affected_target": "digestive system neoplasm",
"target_kind": "disease",
"mechanism": "complex"
} | 0.825813 |
co_coun_00010 | counterfactual | coding_variant | hard | 4 | If MYC were knocked out, its physical interaction with MAPK1 would be lost. Which pathway of MAPK1 could therefore be indirectly affected? | MYC GENE_ENCODES_PROTEIN MYC -> MYC PROTEIN_PHYSICALLY_INTERACTS_WITH MAPK1 -> MAPK1 GENE_ENCODES_PROTEIN MAPK1 -> MAPK1 GENE_PARTICIPATES_IN_PATHWAY RHO GTPases Activate WASPs and WAVEs | {
"steps": [
{
"hop": 1,
"source_node_id": "MYC",
"source_node_type": "GENE",
"source_node_label": "MYC",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "4609",
... | RHO GTPases Activate WASPs and WAVEs | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MYC",
"source_db": "UniProt",
"payload": {
"accession": "P01106",
"sequence": "MDFFRVVENQQPPATMPLNVSFTNRNYDLDYDSVQPYFYCDEEENFYQQQQQSELQPPAPSEDIWKKFELLPTPPLSPSRRSGLCSPSYVAVTPFSLRGDNDGGGGSFSTADQLEMVTELLGGDMVNQSFICDPD... | [
{
"source_db": "bridge",
"source_id": "4609",
"text": "MYC GENE_ENCODES_PROTEIN MYC",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "5594",
"text": "MYC PROTEIN_PHYSICALLY_INTERACTS_WITH MAPK1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": ... | {
"knocked_out_gene": "MYC",
"interaction_partner": "MAPK1",
"affected_target": "RHO GTPases Activate WASPs and WAVEs",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00011 | counterfactual | coding_variant | hard | 4 | If CREBBP were knocked out, its physical interaction with CDH1 would be lost. Which disease association of CDH1 could therefore be indirectly affected? | CREBBP GENE_ENCODES_PROTEIN CREBBP -> CREBBP PROTEIN_PHYSICALLY_INTERACTS_WITH CDH1 -> CDH1 GENE_ENCODES_PROTEIN CDH1 -> CDH1 GENE_ASSOCIATED_WITH_DISEASE hepatobiliary neoplasm | {
"steps": [
{
"hop": 1,
"source_node_id": "CREBBP",
"source_node_type": "GENE",
"source_node_label": "CREBBP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "13... | hepatobiliary neoplasm | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CREBBP",
"source_db": "UniProt",
"payload": {
"accession": "Q92793",
"sequence": "MAENLLDGPPNPKRAKLSSPGFSANDSTDFGSLFDLENDLPDELIPNGGELGLLNSGNLVPDAASKHKQLSELLRGGSGSSINPGIGNVSASSPVQQGLGGQAQGQPNSANMASLSAMGKSPLSQGDSSAPS... | [
{
"source_db": "bridge",
"source_id": "1387",
"text": "CREBBP GENE_ENCODES_PROTEIN CREBBP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "999",
"text": "CREBBP PROTEIN_PHYSICALLY_INTERACTS_WITH CDH1",
"confidence": 0.9
},
{
"source_db": "bridge",
"sourc... | {
"knocked_out_gene": "CREBBP",
"interaction_partner": "CDH1",
"affected_target": "hepatobiliary neoplasm",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670462 |
co_coun_00012 | counterfactual | coding_variant | hard | 4 | If CDKN1A were knocked out, its physical interaction with ESR1 would be lost. Which disease association of ESR1 could therefore be indirectly affected? | CDKN1A GENE_ENCODES_PROTEIN CDKN1A -> CDKN1A PROTEIN_PHYSICALLY_INTERACTS_WITH ESR1 -> ESR1 GENE_ENCODES_PROTEIN ESR1 -> ESR1 GENE_ASSOCIATED_WITH_DISEASE parathyroid gland carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CDKN1A",
"source_node_type": "GENE",
"source_node_label": "CDKN1A",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "10... | parathyroid gland carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDKN1A",
"source_db": "UniProt",
"payload": {
"accession": "P38936",
"sequence": "MSEPAGDVRQNPCGSKACRRLFGPVDSEQLSRDCDALMAGCIQEARERWNFDFVTETPLEGDFAWERVRGLGLPKLYLPTGPRRGRDELGGGRRPGTSPALLQGTAEEDHVDLSLSCTLVPRSGEQAEGSPG... | [
{
"source_db": "bridge",
"source_id": "1026",
"text": "CDKN1A GENE_ENCODES_PROTEIN CDKN1A",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "2099",
"text": "CDKN1A PROTEIN_PHYSICALLY_INTERACTS_WITH ESR1",
"confidence": 0.9
},
{
"source_db": "bridge",
"sour... | {
"knocked_out_gene": "CDKN1A",
"interaction_partner": "ESR1",
"affected_target": "parathyroid gland carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.675661 |
co_coun_00013 | counterfactual | coding_variant | hard | 4 | If BRAF were knocked out, its physical interaction with AKT1 would be lost. Which pathway of AKT1 could therefore be indirectly affected? | BRAF GENE_ENCODES_PROTEIN BRAF -> BRAF PROTEIN_PHYSICALLY_INTERACTS_WITH AKT1 -> AKT1 GENE_ENCODES_PROTEIN AKT1 -> AKT1 GENE_PARTICIPATES_IN_PATHWAY Regulation of TP53 Degradation | {
"steps": [
{
"hop": 1,
"source_node_id": "BRAF",
"source_node_type": "GENE",
"source_node_label": "BRAF",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "673",
... | Regulation of TP53 Degradation | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRAF",
"source_db": "UniProt",
"payload": {
"accession": "P15056",
"sequence": "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEHIEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTVTSSSSSSLSVLPSS... | [
{
"source_db": "bridge",
"source_id": "673",
"text": "BRAF GENE_ENCODES_PROTEIN BRAF",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "207",
"text": "BRAF PROTEIN_PHYSICALLY_INTERACTS_WITH AKT1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": ... | {
"knocked_out_gene": "BRAF",
"interaction_partner": "AKT1",
"affected_target": "Regulation of TP53 Degradation",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00014 | counterfactual | coding_variant | hard | 4 | If RAD51C were knocked out, its physical interaction with BRCA2 would be lost. Which disease association of BRCA2 could therefore be indirectly affected? | RAD51C GENE_ENCODES_PROTEIN RAD51C -> RAD51C PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA2 -> BRCA2 GENE_ENCODES_PROTEIN BRCA2 -> BRCA2 GENE_ASSOCIATED_WITH_DISEASE kidney Wilms tumor | {
"steps": [
{
"hop": 1,
"source_node_id": "RAD51C",
"source_node_type": "GENE",
"source_node_label": "RAD51C",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "58... | kidney Wilms tumor | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "RAD51C",
"source_db": "UniProt",
"payload": {
"accession": "O43502",
"sequence": "MRGKTFRFEMQRDLVSFPLSPAVRVKLVSAGFQTAEELLEVKPSELSKEVGISKAEALETLQIIRRECLTNKPRYAGTSESHKKCTALELLEQEHTQGFIITFCSALDDILGGGVPLMKTTEICGAPGVGKT... | [
{
"source_db": "bridge",
"source_id": "5889",
"text": "RAD51C GENE_ENCODES_PROTEIN RAD51C",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "675",
"text": "RAD51C PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA2",
"confidence": 0.9
},
{
"source_db": "bridge",
"sour... | {
"knocked_out_gene": "RAD51C",
"interaction_partner": "BRCA2",
"affected_target": "kidney Wilms tumor",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.775867 |
co_coun_00015 | counterfactual | coding_variant | hard | 4 | If LRRK2 were knocked out, its physical interaction with TP53 would be lost. Which disease association of TP53 could therefore be indirectly affected? | LRRK2 GENE_ENCODES_PROTEIN LRRK2 -> LRRK2 PROTEIN_PHYSICALLY_INTERACTS_WITH TP53 -> TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 GENE_ASSOCIATED_WITH_DISEASE esophageal cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "LRRK2",
"source_node_type": "GENE",
"source_node_label": "LRRK2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "1208... | esophageal cancer | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "LRRK2",
"source_db": "UniProt",
"payload": {
"accession": "Q5S007",
"sequence": "MASGSCQGCEEDEETLKKLIVRLNNVQEGKQIETLVQILEDLLVFTYSERASKLFQGKNIHVPLLIVLDSYMRVASVQQVGWSLLCKLIEVCPGTMQSLMGPQDVGNDWEVLGVHQLILKMLTVHNASVNLSV... | [
{
"source_db": "bridge",
"source_id": "120892",
"text": "LRRK2 GENE_ENCODES_PROTEIN LRRK2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "7157",
"text": "LRRK2 PROTEIN_PHYSICALLY_INTERACTS_WITH TP53",
"confidence": 0.9
},
{
"source_db": "bridge",
"sourc... | {
"knocked_out_gene": "LRRK2",
"interaction_partner": "TP53",
"affected_target": "esophageal cancer",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00016 | counterfactual | coding_variant | hard | 4 | If NF1 were knocked out, its physical interaction with ESR1 would be lost. Which disease association of ESR1 could therefore be indirectly affected? | NF1 GENE_ENCODES_PROTEIN NF1 -> NF1 PROTEIN_PHYSICALLY_INTERACTS_WITH ESR1 -> ESR1 GENE_ENCODES_PROTEIN ESR1 -> ESR1 GENE_ASSOCIATED_WITH_DISEASE ovarian carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "NF1",
"source_node_type": "GENE",
"source_node_label": "NF1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "4763",
... | ovarian carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NF1",
"source_db": "UniProt",
"payload": {
"accession": "P21359",
"sequence": "MAAHRPVEWVQAVVSRFDEQLPIKTGQQNTHTKVSTEHNKECLINISKYKFSLVISGLTTILKNVNNMRIFGEAAEKNLYLSQLIILDTLEKCLAGQPKDTMRLDETMLVKQLLPEICHFLHTCREGNQHAAELR... | [
{
"source_db": "bridge",
"source_id": "4763",
"text": "NF1 GENE_ENCODES_PROTEIN NF1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "2099",
"text": "NF1 PROTEIN_PHYSICALLY_INTERACTS_WITH ESR1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "... | {
"knocked_out_gene": "NF1",
"interaction_partner": "ESR1",
"affected_target": "ovarian carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.720044 |
co_coun_00017 | counterfactual | coding_variant | medium | 3 | If ABL1 were knocked out, the BRCA1-cABL complex complex would lose one of its members, indirectly affecting BRCA1, another member of the same complex. Which pathway of BRCA1 could therefore be indirectly affected? | ABL1 PROTEIN_MEMBER_OF_COMPLEX BRCA1-cABL complex -> BRCA1 PROTEIN_MEMBER_OF_COMPLEX BRCA1-cABL complex -> BRCA1 GENE_PARTICIPATES_IN_PATHWAY SUMOylation of DNA damage response and repair proteins | {
"steps": [
{
"hop": 1,
"source_node_id": "ABL1",
"source_node_type": "GENE",
"source_node_label": "ABL1",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "CO... | SUMOylation of DNA damage response and repair proteins | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ABL1",
"source_db": "UniProt",
"payload": {
"accession": "P00519",
"sequence": "MLEICLKLVGCKSKKGLSSSSSCYLEEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHSWYHGPVSR... | [
{
"source_db": "OmniPath",
"source_id": "CORUM:2811",
"text": "ABL1 PROTEIN_MEMBER_OF_COMPLEX BRCA1-cABL complex",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "BRCA1",
"text": "BRCA1 PROTEIN_MEMBER_OF_COMPLEX BRCA1-cABL complex",
"confidence": 1
},
{
"sourc... | {
"knocked_out_gene": "ABL1",
"disrupted_complex": "BRCA1-cABL complex",
"complex_partner": "BRCA1",
"affected_target": "SUMOylation of DNA damage response and repair proteins",
"target_kind": "pathway",
"mechanism": "complex"
} | 1 |
co_coun_00018 | counterfactual | coding_variant | hard | 4 | If BARD1 were knocked out, its physical interaction with BRCA1 would be lost. Which pathway of BRCA1 could therefore be indirectly affected? | BARD1 GENE_ENCODES_PROTEIN BARD1 -> BARD1 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1 -> BRCA1 GENE_ENCODES_PROTEIN BRCA1 -> BRCA1 GENE_PARTICIPATES_IN_PATHWAY TP53 Regulates Transcription of DNA Repair Genes | {
"steps": [
{
"hop": 1,
"source_node_id": "BARD1",
"source_node_type": "GENE",
"source_node_label": "BARD1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "580"... | TP53 Regulates Transcription of DNA Repair Genes | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BARD1",
"source_db": "UniProt",
"payload": {
"accession": "Q99728",
"sequence": "MPDNRQPRNRQPRIRSGNEPRSAPAMEPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQDLKINRQLDSMIQLCSKLRNLLHDNELSDLKEDKPRKSLF... | [
{
"source_db": "bridge",
"source_id": "580",
"text": "BARD1 GENE_ENCODES_PROTEIN BARD1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "672",
"text": "BARD1 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "BARD1",
"interaction_partner": "BRCA1",
"affected_target": "TP53 Regulates Transcription of DNA Repair Genes",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00019 | counterfactual | coding_variant | hard | 4 | If MYC were knocked out, its physical interaction with TUBA4A would be lost. Which disease association of TUBA4A could therefore be indirectly affected? | MYC GENE_ENCODES_PROTEIN MYC -> MYC PROTEIN_PHYSICALLY_INTERACTS_WITH TUBA4A -> TUBA4A GENE_ENCODES_PROTEIN TUBA4A -> TUBA4A GENE_ASSOCIATED_WITH_DISEASE hypopharyngeal carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "MYC",
"source_node_type": "GENE",
"source_node_label": "MYC",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "4609",
... | hypopharyngeal carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MYC",
"source_db": "UniProt",
"payload": {
"accession": "P01106",
"sequence": "MDFFRVVENQQPPATMPLNVSFTNRNYDLDYDSVQPYFYCDEEENFYQQQQQSELQPPAPSEDIWKKFELLPTPPLSPSRRSGLCSPSYVAVTPFSLRGDNDGGGGSFSTADQLEMVTELLGGDMVNQSFICDPD... | [
{
"source_db": "bridge",
"source_id": "4609",
"text": "MYC GENE_ENCODES_PROTEIN MYC",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "7277",
"text": "MYC PROTEIN_PHYSICALLY_INTERACTS_WITH TUBA4A",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "MYC",
"interaction_partner": "TUBA4A",
"affected_target": "hypopharyngeal carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.707597 |
co_coun_00020 | counterfactual | coding_variant | hard | 4 | If PIK3CA were knocked out, its physical interaction with EGFR would be lost. Which disease association of EGFR could therefore be indirectly affected? | PIK3CA GENE_ENCODES_PROTEIN PIK3CA -> PIK3CA PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR -> EGFR GENE_ENCODES_PROTEIN EGFR -> EGFR GENE_ASSOCIATED_WITH_DISEASE Merkel cell skin cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "PIK3CA",
"source_node_type": "GENE",
"source_node_label": "PIK3CA",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "52... | Merkel cell skin cancer | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PIK3CA",
"source_db": "UniProt",
"payload": {
"accession": "P42336",
"sequence": "MPPRPSSGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVK... | [
{
"source_db": "bridge",
"source_id": "5290",
"text": "PIK3CA GENE_ENCODES_PROTEIN PIK3CA",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1956",
"text": "PIK3CA PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR",
"confidence": 0.9
},
{
"source_db": "bridge",
"sour... | {
"knocked_out_gene": "PIK3CA",
"interaction_partner": "EGFR",
"affected_target": "Merkel cell skin cancer",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.673773 |
co_coun_00021 | counterfactual | coding_variant | hard | 4 | If ABL1 were knocked out, its physical interaction with ATM would be lost. Which disease association of ATM could therefore be indirectly affected? | ABL1 GENE_ENCODES_PROTEIN ABL1 -> ABL1 PROTEIN_PHYSICALLY_INTERACTS_WITH ATM -> ATM GENE_ENCODES_PROTEIN ATM -> ATM GENE_ASSOCIATED_WITH_DISEASE familial colorectal cancer type X | {
"steps": [
{
"hop": 1,
"source_node_id": "ABL1",
"source_node_type": "GENE",
"source_node_label": "ABL1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "25",
... | familial colorectal cancer type X | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ABL1",
"source_db": "UniProt",
"payload": {
"accession": "P00519",
"sequence": "MLEICLKLVGCKSKKGLSSSSSCYLEEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHSWYHGPVSR... | [
{
"source_db": "bridge",
"source_id": "25",
"text": "ABL1 GENE_ENCODES_PROTEIN ABL1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "472",
"text": "ABL1 PROTEIN_PHYSICALLY_INTERACTS_WITH ATM",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "A... | {
"knocked_out_gene": "ABL1",
"interaction_partner": "ATM",
"affected_target": "familial colorectal cancer type X",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.827482 |
co_coun_00022 | counterfactual | coding_variant | hard | 4 | If AR were knocked out, its physical interaction with BCOR would be lost. Which disease association of BCOR could therefore be indirectly affected? | AR GENE_ENCODES_PROTEIN AR -> AR PROTEIN_PHYSICALLY_INTERACTS_WITH BCOR -> BCOR GENE_ENCODES_PROTEIN BCOR -> BCOR GENE_ASSOCIATED_WITH_DISEASE goblet cell carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "AR",
"source_node_type": "GENE",
"source_node_label": "AR",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "367",
... | goblet cell carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AR",
"source_db": "UniProt",
"payload": {
"accession": "P10275",
"sequence": "MEVQLGLGRVYPRPPSKTYRGAFQNLFQSVREVIQNPGPRHPEAASAAPPGASLLLLQQQQQQQQQQQQQQQQQQQQQQQETSPRQQQQQQGEDGSPQAHRRGPTGYLVLDEEQQPSQPQSALECHPERGCVPEPG... | [
{
"source_db": "bridge",
"source_id": "367",
"text": "AR GENE_ENCODES_PROTEIN AR",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "54880",
"text": "AR PROTEIN_PHYSICALLY_INTERACTS_WITH BCOR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "BCO... | {
"knocked_out_gene": "AR",
"interaction_partner": "BCOR",
"affected_target": "goblet cell carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670462 |
co_coun_00023 | counterfactual | coding_variant | hard | 4 | If CDK4 were knocked out, its physical interaction with BRCA1 would be lost. Which disease association of BRCA1 could therefore be indirectly affected? | CDK4 GENE_ENCODES_PROTEIN CDK4 -> CDK4 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1 -> BRCA1 GENE_ENCODES_PROTEIN BRCA1 -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE ovarian seromucinous carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CDK4",
"source_node_type": "GENE",
"source_node_label": "CDK4",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "1019",... | ovarian seromucinous carcinoma | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDK4",
"source_db": "UniProt",
"payload": {
"accession": "P11802",
"sequence": "MATSRYEPVAEIGVGAYGTVYKARDPHSGHFVALKSVRVPNGGGGGGGLPISTVREVALLRRLEAFEHPNVVRLMDVCATSRTDREIKVTLVFEHVDQDLRTYLDKAPPPGLPAETIKDLMRQFLRGLDFLHAN... | [
{
"source_db": "bridge",
"source_id": "1019",
"text": "CDK4 GENE_ENCODES_PROTEIN CDK4",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "672",
"text": "CDK4 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"knocked_out_gene": "CDK4",
"interaction_partner": "BRCA1",
"affected_target": "ovarian seromucinous carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670462 |
co_coun_00024 | counterfactual | coding_variant | hard | 4 | If TP53 were knocked out, its physical interaction with ABL1 would be lost. Which disease association of ABL1 could therefore be indirectly affected? | TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 PROTEIN_PHYSICALLY_INTERACTS_WITH ABL1 -> ABL1 GENE_ENCODES_PROTEIN ABL1 -> ABL1 GENE_ASSOCIATED_WITH_DISEASE Ascending tubular aorta aneurysm | {
"steps": [
{
"hop": 1,
"source_node_id": "TP53",
"source_node_type": "GENE",
"source_node_label": "TP53",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "7157",... | Ascending tubular aorta aneurysm | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TP53",
"source_db": "UniProt",
"payload": {
"accession": "P04637",
"sequence": "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMF... | [
{
"source_db": "bridge",
"source_id": "7157",
"text": "TP53 GENE_ENCODES_PROTEIN TP53",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "25",
"text": "TP53 PROTEIN_PHYSICALLY_INTERACTS_WITH ABL1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": ... | {
"knocked_out_gene": "TP53",
"interaction_partner": "ABL1",
"affected_target": "Ascending tubular aorta aneurysm",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.761792 |
co_coun_00025 | counterfactual | coding_variant | hard | 4 | If CSF1R were knocked out, its physical interaction with CBL would be lost. Which disease association of CBL could therefore be indirectly affected? | CSF1R GENE_ENCODES_PROTEIN CSF1R -> CSF1R PROTEIN_PHYSICALLY_INTERACTS_WITH CBL -> CBL GENE_ENCODES_PROTEIN CBL -> CBL GENE_ASSOCIATED_WITH_DISEASE diffuse gastric adenocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CSF1R",
"source_node_type": "GENE",
"source_node_label": "CSF1R",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "1436... | diffuse gastric adenocarcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CSF1R",
"source_db": "UniProt",
"payload": {
"accession": "P07333",
"sequence": "MGPGVLLLLLVATAWHGQGIPVIEPSVPELVVKPGATVTLRCVGNGSVEWDGPPSPHWTLYSDGSSSILSTNNATFQNTGTYRCTEPGDPLGGSAAIHLYVKDPARPWNVLAQEVVVFEDQDALLPCLLTDPV... | [
{
"source_db": "bridge",
"source_id": "1436",
"text": "CSF1R GENE_ENCODES_PROTEIN CSF1R",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "867",
"text": "CSF1R PROTEIN_PHYSICALLY_INTERACTS_WITH CBL",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id... | {
"knocked_out_gene": "CSF1R",
"interaction_partner": "CBL",
"affected_target": "diffuse gastric adenocarcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.605831 |
co_coun_00026 | counterfactual | coding_variant | hard | 4 | If ESR1 were knocked out, its physical interaction with EGFR would be lost. Which disease association of EGFR could therefore be indirectly affected? | ESR1 GENE_ENCODES_PROTEIN ESR1 -> ESR1 PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR -> EGFR GENE_ENCODES_PROTEIN EGFR -> EGFR GENE_ASSOCIATED_WITH_DISEASE pancreatic adenocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "ESR1",
"source_node_type": "GENE",
"source_node_label": "ESR1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "2099",... | pancreatic adenocarcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ESR1",
"source_db": "UniProt",
"payload": {
"accession": "P03372",
"sequence": "MTMTLHTKASGMALLHQIQGNELEPLNRPQLKIPLERPLGEVYLDSSKPAVYNYPEGAAYEFNAAAAANAQVYGQTGLPYGPGSEAAAFGSNGLGGFPPLNSVSPSPLMLLHPPPQLSPFLQPHGQQVPYYLEN... | [
{
"source_db": "bridge",
"source_id": "2099",
"text": "ESR1 GENE_ENCODES_PROTEIN ESR1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1956",
"text": "ESR1 PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"knocked_out_gene": "ESR1",
"interaction_partner": "EGFR",
"affected_target": "pancreatic adenocarcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.71615 |
co_coun_00027 | counterfactual | coding_variant | hard | 4 | If ACVR1B were knocked out, its physical interaction with ACVR1 would be lost. Which disease association of ACVR1 could therefore be indirectly affected? | ACVR1B GENE_ENCODES_PROTEIN ACVR1B -> ACVR1B PROTEIN_PHYSICALLY_INTERACTS_WITH ACVR1 -> ACVR1 GENE_ENCODES_PROTEIN ACVR1 -> ACVR1 GENE_ASSOCIATED_WITH_DISEASE breast lobular carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "ACVR1B",
"source_node_type": "GENE",
"source_node_label": "ACVR1B",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "91... | breast lobular carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACVR1B",
"source_db": "UniProt",
"payload": {
"accession": "P36896",
"sequence": "MAESAGASSFFPLVVLLLAGSGGSGPRGVQALLCACTSCLQANYTCETDGACMVSIFNLDGMEHHVRTCIPKVELVPAGKPFYCLSSEDLRNTHCCYTDYCNRIDLRVPSGHLKEPEHPSMWGPVELVGIIA... | [
{
"source_db": "bridge",
"source_id": "91",
"text": "ACVR1B GENE_ENCODES_PROTEIN ACVR1B",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "90",
"text": "ACVR1B PROTEIN_PHYSICALLY_INTERACTS_WITH ACVR1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_... | {
"knocked_out_gene": "ACVR1B",
"interaction_partner": "ACVR1",
"affected_target": "breast lobular carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670462 |
co_coun_00028 | counterfactual | coding_variant | hard | 4 | If SOX2 were knocked out, its physical interaction with AKT1 would be lost. Which disease association of AKT1 could therefore be indirectly affected? | SOX2 GENE_ENCODES_PROTEIN SOX2 -> SOX2 PROTEIN_PHYSICALLY_INTERACTS_WITH AKT1 -> AKT1 GENE_ENCODES_PROTEIN AKT1 -> AKT1 GENE_ASSOCIATED_WITH_DISEASE clear cell adenocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "SOX2",
"source_node_type": "GENE",
"source_node_label": "SOX2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "6657",... | clear cell adenocarcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SOX2",
"source_db": "UniProt",
"payload": {
"accession": "P48431",
"sequence": "MYNMMETELKPPGPQQTSGGGGGNSTAAAAGGNQKNSPDRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKTLMKKDKYTLPGGLLAP... | [
{
"source_db": "bridge",
"source_id": "6657",
"text": "SOX2 GENE_ENCODES_PROTEIN SOX2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "207",
"text": "SOX2 PROTEIN_PHYSICALLY_INTERACTS_WITH AKT1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "SOX2",
"interaction_partner": "AKT1",
"affected_target": "clear cell adenocarcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.672173 |
co_coun_00029 | counterfactual | coding_variant | hard | 4 | If ATM were knocked out, its physical interaction with PTEN would be lost. Which disease association of PTEN could therefore be indirectly affected? | ATM GENE_ENCODES_PROTEIN ATM -> ATM PROTEIN_PHYSICALLY_INTERACTS_WITH PTEN -> PTEN GENE_ENCODES_PROTEIN PTEN -> PTEN GENE_ASSOCIATED_WITH_DISEASE cervical endometrioid adenocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "ATM",
"source_node_type": "GENE",
"source_node_label": "ATM",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "472",
... | cervical endometrioid adenocarcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ATM",
"source_db": "UniProt",
"payload": {
"accession": "Q13315",
"sequence": "MSLVLNDLLICCRQLEHDRATERKKEVEKFKRLIRDPETIKHLDRHSDSKQGKYLNWDAVFRFLQKYIQKETECLRIAKPNVSASTQASRQKKMQEISSLVKYFIKCANRRAPRLKCQELLNYIMDTVKDSSNGA... | [
{
"source_db": "bridge",
"source_id": "472",
"text": "ATM GENE_ENCODES_PROTEIN ATM",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "5728",
"text": "ATM PROTEIN_PHYSICALLY_INTERACTS_WITH PTEN",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "P... | {
"knocked_out_gene": "ATM",
"interaction_partner": "PTEN",
"affected_target": "cervical endometrioid adenocarcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.671076 |
co_coun_00030 | counterfactual | coding_variant | hard | 4 | If KRAS were knocked out, its physical interaction with NOTCH1 would be lost. Which disease association of NOTCH1 could therefore be indirectly affected? | KRAS GENE_ENCODES_PROTEIN KRAS -> KRAS PROTEIN_PHYSICALLY_INTERACTS_WITH NOTCH1 -> NOTCH1 GENE_ENCODES_PROTEIN NOTCH1 -> NOTCH1 GENE_ASSOCIATED_WITH_DISEASE Chronic Eosinophilic Leukemia, Not Otherwise Specified | {
"steps": [
{
"hop": 1,
"source_node_id": "KRAS",
"source_node_type": "GENE",
"source_node_label": "KRAS",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "3845",... | Chronic Eosinophilic Leukemia, Not Otherwise Specified | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KRAS",
"source_db": "UniProt",
"payload": {
"accession": "P01116",
"sequence": "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLA... | [
{
"source_db": "bridge",
"source_id": "3845",
"text": "KRAS GENE_ENCODES_PROTEIN KRAS",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "4851",
"text": "KRAS PROTEIN_PHYSICALLY_INTERACTS_WITH NOTCH1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "KRAS",
"interaction_partner": "NOTCH1",
"affected_target": "Chronic Eosinophilic Leukemia, Not Otherwise Specified",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670462 |
co_coun_00031 | counterfactual | coding_variant | hard | 4 | If AR were knocked out, its physical interaction with CTNNB1 would be lost. Which disease association of CTNNB1 could therefore be indirectly affected? | AR GENE_ENCODES_PROTEIN AR -> AR PROTEIN_PHYSICALLY_INTERACTS_WITH CTNNB1 -> CTNNB1 GENE_ENCODES_PROTEIN CTNNB1 -> CTNNB1 GENE_ASSOCIATED_WITH_DISEASE urothelial carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "AR",
"source_node_type": "GENE",
"source_node_label": "AR",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "367",
... | urothelial carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AR",
"source_db": "UniProt",
"payload": {
"accession": "P10275",
"sequence": "MEVQLGLGRVYPRPPSKTYRGAFQNLFQSVREVIQNPGPRHPEAASAAPPGASLLLLQQQQQQQQQQQQQQQQQQQQQQQETSPRQQQQQQGEDGSPQAHRRGPTGYLVLDEEQQPSQPQSALECHPERGCVPEPG... | [
{
"source_db": "bridge",
"source_id": "367",
"text": "AR GENE_ENCODES_PROTEIN AR",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1499",
"text": "AR PROTEIN_PHYSICALLY_INTERACTS_WITH CTNNB1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "CT... | {
"knocked_out_gene": "AR",
"interaction_partner": "CTNNB1",
"affected_target": "urothelial carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.673171 |
co_coun_00032 | counterfactual | coding_variant | hard | 4 | If KRAS were knocked out, its physical interaction with PIK3CA would be lost. Which disease association of PIK3CA could therefore be indirectly affected? | KRAS GENE_ENCODES_PROTEIN KRAS -> KRAS PROTEIN_PHYSICALLY_INTERACTS_WITH PIK3CA -> PIK3CA GENE_ENCODES_PROTEIN PIK3CA -> PIK3CA GENE_ASSOCIATED_WITH_DISEASE cervical intraepithelial neoplasia | {
"steps": [
{
"hop": 1,
"source_node_id": "KRAS",
"source_node_type": "GENE",
"source_node_label": "KRAS",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "3845",... | cervical intraepithelial neoplasia | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KRAS",
"source_db": "UniProt",
"payload": {
"accession": "P01116",
"sequence": "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLA... | [
{
"source_db": "bridge",
"source_id": "3845",
"text": "KRAS GENE_ENCODES_PROTEIN KRAS",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "5290",
"text": "KRAS PROTEIN_PHYSICALLY_INTERACTS_WITH PIK3CA",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "KRAS",
"interaction_partner": "PIK3CA",
"affected_target": "cervical intraepithelial neoplasia",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.671914 |
co_coun_00033 | counterfactual | coding_variant | hard | 4 | If CDC25B were knocked out, its physical interaction with AR would be lost. Which disease association of AR could therefore be indirectly affected? | CDC25B GENE_ENCODES_PROTEIN CDC25B -> CDC25B PROTEIN_PHYSICALLY_INTERACTS_WITH AR -> AR GENE_ENCODES_PROTEIN AR -> AR GENE_ASSOCIATED_WITH_DISEASE breast carcinoma by gene expression profile | {
"steps": [
{
"hop": 1,
"source_node_id": "CDC25B",
"source_node_type": "GENE",
"source_node_label": "CDC25B",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "99... | breast carcinoma by gene expression profile | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDC25B",
"source_db": "UniProt",
"payload": {
"accession": "P30305",
"sequence": "MEVPQPEPAPGSALSPAGVCGGAQRPGHLPGLLLGSHGLLGSPVRAAASSPVTTLTQTMHDLAGLGSETPKSQVGTLLFRSRSRLTHLSLSRRASESSLSSESSESSDAGLCMDSPSPMDPHMAEQTFEQAI... | [
{
"source_db": "bridge",
"source_id": "994",
"text": "CDC25B GENE_ENCODES_PROTEIN CDC25B",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "367",
"text": "CDC25B PROTEIN_PHYSICALLY_INTERACTS_WITH AR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "CDC25B",
"interaction_partner": "AR",
"affected_target": "breast carcinoma by gene expression profile",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670462 |
co_coun_00034 | counterfactual | coding_variant | hard | 3 | If ERG were knocked out, the ribonucleoprotein complex complex would lose one of its members, indirectly affecting BRCA1, another member of the same complex. Which disease association of BRCA1 could therefore be indirectly affected? | ERG PROTEIN_MEMBER_OF_COMPLEX ribonucleoprotein complex -> BRCA1 PROTEIN_MEMBER_OF_COMPLEX ribonucleoprotein complex -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE metastatic malignant neoplasm in the lymph nodes | {
"steps": [
{
"hop": 1,
"source_node_id": "ERG",
"source_node_type": "GENE",
"source_node_label": "ERG",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "Comp... | metastatic malignant neoplasm in the lymph nodes | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ERG",
"source_db": "UniProt",
"payload": {
"accession": "P11308",
"sequence": "MASTIKEALSVVSEDQSLFECAYGTPHLAKTEMTASSSSDYGQTSKMSPRVPQQDWLSQPPARVTIKMECNPSQVNGSRNSPDECSVAKGGKMVGSPDTVGMNYGSYMEEKHMPPPNMTTNERRVIVPADPTLWS... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC393",
"text": "ERG PROTEIN_MEMBER_OF_COMPLEX ribonucleoprotein complex",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "BRCA1",
"text": "BRCA1 PROTEIN_MEMBER_OF_COMPLEX ribonucleoprotein complex",
"confidence": 1
... | {
"knocked_out_gene": "ERG",
"disrupted_complex": "ribonucleoprotein complex",
"complex_partner": "BRCA1",
"affected_target": "metastatic malignant neoplasm in the lymph nodes",
"target_kind": "disease",
"mechanism": "complex"
} | 0.794126 |
co_coun_00035 | counterfactual | coding_variant | hard | 4 | If CDH1 were knocked out, its physical interaction with MET would be lost. Which disease association of MET could therefore be indirectly affected? | CDH1 GENE_ENCODES_PROTEIN CDH1 -> CDH1 PROTEIN_PHYSICALLY_INTERACTS_WITH MET -> MET GENE_ENCODES_PROTEIN MET -> MET GENE_ASSOCIATED_WITH_DISEASE kidney oncocytoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CDH1",
"source_node_type": "GENE",
"source_node_label": "CDH1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "999",
... | kidney oncocytoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDH1",
"source_db": "UniProt",
"payload": {
"accession": "P12830",
"sequence": "MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHLERGRVLGRVNFEDCTGRQRTAYFSLDTRFKVGTDGVITVKRPLRFHNPQIHFLVYAWDSTYRKFSTKVTLNTVGHHHRPPPHQASVSG... | [
{
"source_db": "bridge",
"source_id": "999",
"text": "CDH1 GENE_ENCODES_PROTEIN CDH1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "4233",
"text": "CDH1 PROTEIN_PHYSICALLY_INTERACTS_WITH MET",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": ... | {
"knocked_out_gene": "CDH1",
"interaction_partner": "MET",
"affected_target": "kidney oncocytoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670462 |
co_coun_00036 | counterfactual | coding_variant | hard | 4 | If NF1 were knocked out, its physical interaction with ESR1 would be lost. Which disease association of ESR1 could therefore be indirectly affected? | NF1 GENE_ENCODES_PROTEIN NF1 -> NF1 PROTEIN_PHYSICALLY_INTERACTS_WITH ESR1 -> ESR1 GENE_ENCODES_PROTEIN ESR1 -> ESR1 GENE_ASSOCIATED_WITH_DISEASE carcinoma of esophagus | {
"steps": [
{
"hop": 1,
"source_node_id": "NF1",
"source_node_type": "GENE",
"source_node_label": "NF1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "4763",
... | carcinoma of esophagus | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NF1",
"source_db": "UniProt",
"payload": {
"accession": "P21359",
"sequence": "MAAHRPVEWVQAVVSRFDEQLPIKTGQQNTHTKVSTEHNKECLINISKYKFSLVISGLTTILKNVNNMRIFGEAAEKNLYLSQLIILDTLEKCLAGQPKDTMRLDETMLVKQLLPEICHFLHTCREGNQHAAELR... | [
{
"source_db": "bridge",
"source_id": "4763",
"text": "NF1 GENE_ENCODES_PROTEIN NF1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "2099",
"text": "NF1 PROTEIN_PHYSICALLY_INTERACTS_WITH ESR1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "... | {
"knocked_out_gene": "NF1",
"interaction_partner": "ESR1",
"affected_target": "carcinoma of esophagus",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.676174 |
co_coun_00037 | counterfactual | coding_variant | hard | 4 | If ERBB2 were knocked out, its physical interaction with EGFR would be lost. Which disease association of EGFR could therefore be indirectly affected? | ERBB2 GENE_ENCODES_PROTEIN ERBB2 -> ERBB2 PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR -> EGFR GENE_ENCODES_PROTEIN EGFR -> EGFR GENE_ASSOCIATED_WITH_DISEASE glioma | {
"steps": [
{
"hop": 1,
"source_node_id": "ERBB2",
"source_node_type": "GENE",
"source_node_label": "ERBB2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "2064... | glioma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ERBB2",
"source_db": "UniProt",
"payload": {
"accession": "P04626",
"sequence": "MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGAS... | [
{
"source_db": "bridge",
"source_id": "2064",
"text": "ERBB2 GENE_ENCODES_PROTEIN ERBB2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1956",
"text": "ERBB2 PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_... | {
"knocked_out_gene": "ERBB2",
"interaction_partner": "EGFR",
"affected_target": "glioma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00038 | counterfactual | coding_variant | hard | 4 | If APP were knocked out, its physical interaction with KRAS would be lost. Which disease association of KRAS could therefore be indirectly affected? | APP GENE_ENCODES_PROTEIN APP -> APP PROTEIN_PHYSICALLY_INTERACTS_WITH KRAS -> KRAS GENE_ENCODES_PROTEIN KRAS -> KRAS GENE_ASSOCIATED_WITH_DISEASE malignant pancreatic neoplasm | {
"steps": [
{
"hop": 1,
"source_node_id": "APP",
"source_node_type": "GENE",
"source_node_label": "APP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "351",
... | malignant pancreatic neoplasm | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APP",
"source_db": "UniProt",
"payload": {
"accession": "P05067",
"sequence": "MLPGLALLLLAAWTARALEVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGILQYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKF... | [
{
"source_db": "bridge",
"source_id": "351",
"text": "APP GENE_ENCODES_PROTEIN APP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "3845",
"text": "APP PROTEIN_PHYSICALLY_INTERACTS_WITH KRAS",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "K... | {
"knocked_out_gene": "APP",
"interaction_partner": "KRAS",
"affected_target": "malignant pancreatic neoplasm",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.756842 |
co_coun_00039 | counterfactual | coding_variant | hard | 4 | If TP53 were knocked out, its physical interaction with ESR1 would be lost. Which disease association of ESR1 could therefore be indirectly affected? | TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 PROTEIN_PHYSICALLY_INTERACTS_WITH ESR1 -> ESR1 GENE_ENCODES_PROTEIN ESR1 -> ESR1 GENE_ASSOCIATED_WITH_DISEASE escherichia coli infection | {
"steps": [
{
"hop": 1,
"source_node_id": "TP53",
"source_node_type": "GENE",
"source_node_label": "TP53",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "7157",... | escherichia coli infection | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TP53",
"source_db": "UniProt",
"payload": {
"accession": "P04637",
"sequence": "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMF... | [
{
"source_db": "bridge",
"source_id": "7157",
"text": "TP53 GENE_ENCODES_PROTEIN TP53",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "2099",
"text": "TP53 PROTEIN_PHYSICALLY_INTERACTS_WITH ESR1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"knocked_out_gene": "TP53",
"interaction_partner": "ESR1",
"affected_target": "escherichia coli infection",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.694333 |
co_coun_00040 | counterfactual | coding_variant | hard | 4 | If CD2AP were knocked out, its physical interaction with EGFR would be lost. Which disease association of EGFR could therefore be indirectly affected? | CD2AP GENE_ENCODES_PROTEIN CD2AP -> CD2AP PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR -> EGFR GENE_ENCODES_PROTEIN EGFR -> EGFR GENE_ASSOCIATED_WITH_DISEASE gastric carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CD2AP",
"source_node_type": "GENE",
"source_node_label": "CD2AP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "2360... | gastric carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CD2AP",
"source_db": "UniProt",
"payload": {
"accession": "Q9Y5K6",
"sequence": "MVDYIVEYDYDAVHDDELTIRVGEIIRNVKKLQEEGWLEGELNGRRGMFPDNFVKEIKRETEFKDDSLPIKRERHGNVASLVQRISTYGLPAGGIQPHPQTKNIKKKTKKRQCKVLFEYIPQNEDELELKVGD... | [
{
"source_db": "bridge",
"source_id": "23607",
"text": "CD2AP GENE_ENCODES_PROTEIN CD2AP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1956",
"text": "CD2AP PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source... | {
"knocked_out_gene": "CD2AP",
"interaction_partner": "EGFR",
"affected_target": "gastric carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.700043 |
co_coun_00041 | counterfactual | coding_variant | hard | 4 | If MAPT were knocked out, its physical interaction with APOE would be lost. Which disease association of APOE could therefore be indirectly affected? | MAPT GENE_ENCODES_PROTEIN MAPT -> MAPT PROTEIN_PHYSICALLY_INTERACTS_WITH APOE -> APOE GENE_ENCODES_PROTEIN APOE -> APOE GENE_ASSOCIATED_WITH_DISEASE cirrhosis of liver | {
"steps": [
{
"hop": 1,
"source_node_id": "MAPT",
"source_node_type": "GENE",
"source_node_label": "MAPT",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "4137",... | cirrhosis of liver | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MAPT",
"source_db": "UniProt",
"payload": {
"accession": "P10636",
"sequence": "MAEPRQEFEVMEDHAGTYGLGDRKDQGGYTMHQDQEGDTDAGLKESPLQTPTEDGSEEPGSETSDAKSTPTAEDVTAPLVDEGAPGKQAAAQPHTEIPEGTTAEEAGIGDTPSLEDEAAGHVTQEPESGKVVQE... | [
{
"source_db": "bridge",
"source_id": "4137",
"text": "MAPT GENE_ENCODES_PROTEIN MAPT",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "348",
"text": "MAPT PROTEIN_PHYSICALLY_INTERACTS_WITH APOE",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "MAPT",
"interaction_partner": "APOE",
"affected_target": "cirrhosis of liver",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.625088 |
co_coun_00042 | counterfactual | coding_variant | hard | 4 | If KMT2D were knocked out, its physical interaction with CREBBP would be lost. Which pathway of CREBBP could therefore be indirectly affected? | KMT2D GENE_ENCODES_PROTEIN KMT2D -> KMT2D PROTEIN_PHYSICALLY_INTERACTS_WITH CREBBP -> CREBBP GENE_ENCODES_PROTEIN CREBBP -> CREBBP GENE_PARTICIPATES_IN_PATHWAY SARS-CoV-2 activates/modulates innate and adaptive immune responses | {
"steps": [
{
"hop": 1,
"source_node_id": "KMT2D",
"source_node_type": "GENE",
"source_node_label": "KMT2D",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "8085... | SARS-CoV-2 activates/modulates innate and adaptive immune responses | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KMT2D",
"source_db": "UniProt",
"payload": {
"accession": "O14686",
"sequence": "MDSQKLAGEDKDSEPAADGPAASEDPSATESDLPNPHVGEVSVLSSGSPRLQETPQDCSGGPVRRCALCNCGEPSLHGQRELRRFELPFDWPRCPVVSPGGSPGPNEAVLPSEDLSQIGFPEGLTPAHLGEPG... | [
{
"source_db": "bridge",
"source_id": "8085",
"text": "KMT2D GENE_ENCODES_PROTEIN KMT2D",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1387",
"text": "KMT2D PROTEIN_PHYSICALLY_INTERACTS_WITH CREBBP",
"confidence": 0.9
},
{
"source_db": "bridge",
"sourc... | {
"knocked_out_gene": "KMT2D",
"interaction_partner": "CREBBP",
"affected_target": "SARS-CoV-2 activates/modulates innate and adaptive immune responses",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00043 | counterfactual | coding_variant | hard | 4 | If CTNNB1 were knocked out, its physical interaction with APC would be lost. Which disease association of APC could therefore be indirectly affected? | CTNNB1 GENE_ENCODES_PROTEIN CTNNB1 -> CTNNB1 PROTEIN_PHYSICALLY_INTERACTS_WITH APC -> APC GENE_ENCODES_PROTEIN APC -> APC GENE_ASSOCIATED_WITH_DISEASE lung adenocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CTNNB1",
"source_node_type": "GENE",
"source_node_label": "CTNNB1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "14... | lung adenocarcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CTNNB1",
"source_db": "UniProt",
"payload": {
"accession": "P35222",
"sequence": "MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSLSGKGNPEEEDVDTSQVLYEWEQGFSQSFTQEQVADIDGQYAMTRAQRVRAAMFPETLDEGMQIPSTQFDAAHPTNVQRLAEPSQML... | [
{
"source_db": "bridge",
"source_id": "1499",
"text": "CTNNB1 GENE_ENCODES_PROTEIN CTNNB1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "324",
"text": "CTNNB1 PROTEIN_PHYSICALLY_INTERACTS_WITH APC",
"confidence": 0.9
},
{
"source_db": "bridge",
"source... | {
"knocked_out_gene": "CTNNB1",
"interaction_partner": "APC",
"affected_target": "lung adenocarcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.77672 |
co_coun_00044 | counterfactual | coding_variant | hard | 4 | If MET were knocked out, its physical interaction with CBL would be lost. Which disease association of CBL could therefore be indirectly affected? | MET GENE_ENCODES_PROTEIN MET -> MET PROTEIN_PHYSICALLY_INTERACTS_WITH CBL -> CBL GENE_ENCODES_PROTEIN CBL -> CBL GENE_ASSOCIATED_WITH_DISEASE myelodysplastic/myeloproliferative neoplasm | {
"steps": [
{
"hop": 1,
"source_node_id": "MET",
"source_node_type": "GENE",
"source_node_label": "MET",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "4233",
... | myelodysplastic/myeloproliferative neoplasm | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MET",
"source_db": "UniProt",
"payload": {
"accession": "P08581",
"sequence": "MKAPAVLAPGILVLLFTLVQRSNGECKEALAKSEMNVNMKYQLPNFTAETPIQNVILHEHHIFLGATNYIYVLNEEDLQKVAEYKTGPVLEHPDCFPCQDCSSKANLSGGVWKDNINMALVVDTYYDDQLISCGS... | [
{
"source_db": "bridge",
"source_id": "4233",
"text": "MET GENE_ENCODES_PROTEIN MET",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "867",
"text": "MET PROTEIN_PHYSICALLY_INTERACTS_WITH CBL",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "CB... | {
"knocked_out_gene": "MET",
"interaction_partner": "CBL",
"affected_target": "myelodysplastic/myeloproliferative neoplasm",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00045 | counterfactual | coding_variant | hard | 4 | If HTT were knocked out, its physical interaction with EGFR would be lost. Which disease association of EGFR could therefore be indirectly affected? | HTT GENE_ENCODES_PROTEIN HTT -> HTT PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR -> EGFR GENE_ENCODES_PROTEIN EGFR -> EGFR GENE_ASSOCIATED_WITH_DISEASE lung giant cell carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "HTT",
"source_node_type": "GENE",
"source_node_label": "HTT",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "3064",
... | lung giant cell carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "HTT",
"source_db": "UniProt",
"payload": {
"accession": "P42858",
"sequence": "MATLEKLMKAFESLKSFQQQQQQQQQQQQQQQQQQQQQPPPPPPPPPPPQLPQPPPQAQPLLPQPQPPPPPPPPPPGPAVAEEPLHRPKKELSATKKDRVNHCLTICENIVAQSVRNSPEFQKLLGIAMELFLLC... | [
{
"source_db": "bridge",
"source_id": "3064",
"text": "HTT GENE_ENCODES_PROTEIN HTT",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1956",
"text": "HTT PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "... | {
"knocked_out_gene": "HTT",
"interaction_partner": "EGFR",
"affected_target": "lung giant cell carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.672243 |
co_coun_00046 | counterfactual | coding_variant | hard | 4 | If FLT3 were knocked out, its physical interaction with CTNNB1 would be lost. Which disease association of CTNNB1 could therefore be indirectly affected? | FLT3 GENE_ENCODES_PROTEIN FLT3 -> FLT3 PROTEIN_PHYSICALLY_INTERACTS_WITH CTNNB1 -> CTNNB1 GENE_ENCODES_PROTEIN CTNNB1 -> CTNNB1 GENE_ASSOCIATED_WITH_DISEASE pancreatic neuroendocrine tumor | {
"steps": [
{
"hop": 1,
"source_node_id": "FLT3",
"source_node_type": "GENE",
"source_node_label": "FLT3",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "2322",... | pancreatic neuroendocrine tumor | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "FLT3",
"source_db": "UniProt",
"payload": {
"accession": "P36888",
"sequence": "MPALARDGGQLPLLVVFSAMIFGTITNQDLPVIKCVLINHKNNDSSVGKSSSYPMVSESPEDLGCALRPQSSGTVYEAAAVEVDVSASITLQVLVDAPGNISCLWVFKHSSLNCQPHFDLQNRGVVSMVILKMT... | [
{
"source_db": "bridge",
"source_id": "2322",
"text": "FLT3 GENE_ENCODES_PROTEIN FLT3",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1499",
"text": "FLT3 PROTEIN_PHYSICALLY_INTERACTS_WITH CTNNB1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "FLT3",
"interaction_partner": "CTNNB1",
"affected_target": "pancreatic neuroendocrine tumor",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.672598 |
co_coun_00047 | counterfactual | coding_variant | hard | 4 | If CBL were knocked out, its physical interaction with EGFR would be lost. Which disease association of EGFR could therefore be indirectly affected? | CBL GENE_ENCODES_PROTEIN CBL -> CBL PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR -> EGFR GENE_ENCODES_PROTEIN EGFR -> EGFR GENE_ASSOCIATED_WITH_DISEASE prostate cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "CBL",
"source_node_type": "GENE",
"source_node_label": "CBL",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "867",
... | prostate cancer | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CBL",
"source_db": "UniProt",
"payload": {
"accession": "P22681",
"sequence": "MAGNVKKSSGAGGGSGSGGSGSGGLIGLMKDAFQPHHHHHHHLSPHPPGTVDKKMVEKCWKLMDKVVRLCQNPKLALKNSPPYILDLLPDTYQHLRTILSRYEGKMETLGENEYFRVFMENLMKKTKQTISLFKE... | [
{
"source_db": "bridge",
"source_id": "867",
"text": "CBL GENE_ENCODES_PROTEIN CBL",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1956",
"text": "CBL PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "E... | {
"knocked_out_gene": "CBL",
"interaction_partner": "EGFR",
"affected_target": "prostate cancer",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.734847 |
co_coun_00048 | counterfactual | coding_variant | hard | 4 | If NRAS were knocked out, its physical interaction with PIK3CA would be lost. Which disease association of PIK3CA could therefore be indirectly affected? | NRAS GENE_ENCODES_PROTEIN NRAS -> NRAS PROTEIN_PHYSICALLY_INTERACTS_WITH PIK3CA -> PIK3CA GENE_ENCODES_PROTEIN PIK3CA -> PIK3CA GENE_ASSOCIATED_WITH_DISEASE urinary bladder cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "NRAS",
"source_node_type": "GENE",
"source_node_label": "NRAS",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "4893",... | urinary bladder cancer | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NRAS",
"source_db": "UniProt",
"payload": {
"accession": "P01111",
"sequence": "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDLPTRTVDTKQAHELA... | [
{
"source_db": "bridge",
"source_id": "4893",
"text": "NRAS GENE_ENCODES_PROTEIN NRAS",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "5290",
"text": "NRAS PROTEIN_PHYSICALLY_INTERACTS_WITH PIK3CA",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "NRAS",
"interaction_partner": "PIK3CA",
"affected_target": "urinary bladder cancer",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.826665 |
co_coun_00049 | counterfactual | coding_variant | hard | 4 | If ATM were knocked out, its physical interaction with BRCA2 would be lost. Which disease association of BRCA2 could therefore be indirectly affected? | ATM GENE_ENCODES_PROTEIN ATM -> ATM PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA2 -> BRCA2 GENE_ENCODES_PROTEIN BRCA2 -> BRCA2 GENE_ASSOCIATED_WITH_DISEASE papillary serous cystadenocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "ATM",
"source_node_type": "GENE",
"source_node_label": "ATM",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "472",
... | papillary serous cystadenocarcinoma | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ATM",
"source_db": "UniProt",
"payload": {
"accession": "Q13315",
"sequence": "MSLVLNDLLICCRQLEHDRATERKKEVEKFKRLIRDPETIKHLDRHSDSKQGKYLNWDAVFRFLQKYIQKETECLRIAKPNVSASTQASRQKKMQEISSLVKYFIKCANRRAPRLKCQELLNYIMDTVKDSSNGA... | [
{
"source_db": "bridge",
"source_id": "472",
"text": "ATM GENE_ENCODES_PROTEIN ATM",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "675",
"text": "ATM PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA2",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "B... | {
"knocked_out_gene": "ATM",
"interaction_partner": "BRCA2",
"affected_target": "papillary serous cystadenocarcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.728842 |
co_coun_00050 | counterfactual | coding_variant | hard | 4 | If MAPK1 were knocked out, its physical interaction with BRCA1 would be lost. Which disease association of BRCA1 could therefore be indirectly affected? | MAPK1 GENE_ENCODES_PROTEIN MAPK1 -> MAPK1 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1 -> BRCA1 GENE_ENCODES_PROTEIN BRCA1 -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE Familial breast-ovarian cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "MAPK1",
"source_node_type": "GENE",
"source_node_label": "MAPK1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "5594... | Familial breast-ovarian cancer | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MAPK1",
"source_db": "UniProt",
"payload": {
"accession": "P28482",
"sequence": "MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQI... | [
{
"source_db": "bridge",
"source_id": "5594",
"text": "MAPK1 GENE_ENCODES_PROTEIN MAPK1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "672",
"text": "MAPK1 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_... | {
"knocked_out_gene": "MAPK1",
"interaction_partner": "BRCA1",
"affected_target": "Familial breast-ovarian cancer",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00051 | counterfactual | coding_variant | hard | 4 | If APP were knocked out, its physical interaction with PSEN1 would be lost. Which disease association of PSEN1 could therefore be indirectly affected? | APP GENE_ENCODES_PROTEIN APP -> APP PROTEIN_PHYSICALLY_INTERACTS_WITH PSEN1 -> PSEN1 GENE_ENCODES_PROTEIN PSEN1 -> PSEN1 GENE_ASSOCIATED_WITH_DISEASE semantic dementia | {
"steps": [
{
"hop": 1,
"source_node_id": "APP",
"source_node_type": "GENE",
"source_node_label": "APP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "351",
... | semantic dementia | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APP",
"source_db": "UniProt",
"payload": {
"accession": "P05067",
"sequence": "MLPGLALLLLAAWTARALEVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGILQYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKF... | [
{
"source_db": "bridge",
"source_id": "351",
"text": "APP GENE_ENCODES_PROTEIN APP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "5663",
"text": "APP PROTEIN_PHYSICALLY_INTERACTS_WITH PSEN1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "... | {
"knocked_out_gene": "APP",
"interaction_partner": "PSEN1",
"affected_target": "semantic dementia",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.834077 |
co_coun_00052 | counterfactual | coding_variant | hard | 4 | If FBXO7 were knocked out, its physical interaction with AKT1 would be lost. Which disease association of AKT1 could therefore be indirectly affected? | FBXO7 GENE_ENCODES_PROTEIN FBXO7 -> FBXO7 PROTEIN_PHYSICALLY_INTERACTS_WITH AKT1 -> AKT1 GENE_ENCODES_PROTEIN AKT1 -> AKT1 GENE_ASSOCIATED_WITH_DISEASE sebaceous adenoma | {
"steps": [
{
"hop": 1,
"source_node_id": "FBXO7",
"source_node_type": "GENE",
"source_node_label": "FBXO7",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "2579... | sebaceous adenoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "FBXO7",
"source_db": "UniProt",
"payload": {
"accession": "Q9Y3I1",
"sequence": "MRLRVRLLKRTWPLEVPETEPTLGHLRSHLRQSLLCTWGYSSNTRFTITLNYKDPLTGDEETLASYGIVSGDLICLILQDDIPAPNIPSSTDSEHSSLQNNEQPSLATSSNQTSMQDEQPSDSFQGQAAQSGV... | [
{
"source_db": "bridge",
"source_id": "25793",
"text": "FBXO7 GENE_ENCODES_PROTEIN FBXO7",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "207",
"text": "FBXO7 PROTEIN_PHYSICALLY_INTERACTS_WITH AKT1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_... | {
"knocked_out_gene": "FBXO7",
"interaction_partner": "AKT1",
"affected_target": "sebaceous adenoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670462 |
co_coun_00053 | counterfactual | coding_variant | hard | 4 | If BRCA1 were knocked out, its physical interaction with CREBBP would be lost. Which pathway of CREBBP could therefore be indirectly affected? | BRCA1 GENE_ENCODES_PROTEIN BRCA1 -> BRCA1 PROTEIN_PHYSICALLY_INTERACTS_WITH CREBBP -> CREBBP GENE_ENCODES_PROTEIN CREBBP -> CREBBP GENE_PARTICIPATES_IN_PATHWAY Nuclear events mediated by NFE2L2 | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA1",
"source_node_type": "GENE",
"source_node_label": "BRCA1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "672"... | Nuclear events mediated by NFE2L2 | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA1",
"source_db": "UniProt",
"payload": {
"accession": "P38398",
"sequence": "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNR... | [
{
"source_db": "bridge",
"source_id": "672",
"text": "BRCA1 GENE_ENCODES_PROTEIN BRCA1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1387",
"text": "BRCA1 PROTEIN_PHYSICALLY_INTERACTS_WITH CREBBP",
"confidence": 0.9
},
{
"source_db": "bridge",
"source... | {
"knocked_out_gene": "BRCA1",
"interaction_partner": "CREBBP",
"affected_target": "Nuclear events mediated by NFE2L2",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00054 | counterfactual | coding_variant | hard | 4 | If ERBB4 were knocked out, its physical interaction with TP53 would be lost. Which disease association of TP53 could therefore be indirectly affected? | ERBB4 GENE_ENCODES_PROTEIN ERBB4 -> ERBB4 PROTEIN_PHYSICALLY_INTERACTS_WITH TP53 -> TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 GENE_ASSOCIATED_WITH_DISEASE pharyngeal squamous cell carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "ERBB4",
"source_node_type": "GENE",
"source_node_label": "ERBB4",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "2066... | pharyngeal squamous cell carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ERBB4",
"source_db": "UniProt",
"payload": {
"accession": "Q15303",
"sequence": "MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQYRALRKYYENCEVVMGNLEITSIEHNRDLSFLRSVREVTGYVLVALNQFRYLPLENLRIIRGTKLYEDRYALAIFLNYRKDGNFGLQE... | [
{
"source_db": "bridge",
"source_id": "2066",
"text": "ERBB4 GENE_ENCODES_PROTEIN ERBB4",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "7157",
"text": "ERBB4 PROTEIN_PHYSICALLY_INTERACTS_WITH TP53",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_... | {
"knocked_out_gene": "ERBB4",
"interaction_partner": "TP53",
"affected_target": "pharyngeal squamous cell carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.722516 |
co_coun_00055 | counterfactual | coding_variant | hard | 4 | If ABL1 were knocked out, its physical interaction with BRCA1 would be lost. Which disease association of BRCA1 could therefore be indirectly affected? | ABL1 GENE_ENCODES_PROTEIN ABL1 -> ABL1 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1 -> BRCA1 GENE_ENCODES_PROTEIN BRCA1 -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE Carcinoma, Spindle-Cell | {
"steps": [
{
"hop": 1,
"source_node_id": "ABL1",
"source_node_type": "GENE",
"source_node_label": "ABL1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "25",
... | Carcinoma, Spindle-Cell | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ABL1",
"source_db": "UniProt",
"payload": {
"accession": "P00519",
"sequence": "MLEICLKLVGCKSKKGLSSSSSCYLEEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHSWYHGPVSR... | [
{
"source_db": "bridge",
"source_id": "25",
"text": "ABL1 GENE_ENCODES_PROTEIN ABL1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "672",
"text": "ABL1 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": ... | {
"knocked_out_gene": "ABL1",
"interaction_partner": "BRCA1",
"affected_target": "Carcinoma, Spindle-Cell",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.683852 |
co_coun_00056 | counterfactual | coding_variant | hard | 4 | If MYC were knocked out, its physical interaction with TP53 would be lost. Which disease association of TP53 could therefore be indirectly affected? | MYC GENE_ENCODES_PROTEIN MYC -> MYC PROTEIN_PHYSICALLY_INTERACTS_WITH TP53 -> TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 GENE_ASSOCIATED_WITH_DISEASE ependymal tumor | {
"steps": [
{
"hop": 1,
"source_node_id": "MYC",
"source_node_type": "GENE",
"source_node_label": "MYC",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "4609",
... | ependymal tumor | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MYC",
"source_db": "UniProt",
"payload": {
"accession": "P01106",
"sequence": "MDFFRVVENQQPPATMPLNVSFTNRNYDLDYDSVQPYFYCDEEENFYQQQQQSELQPPAPSEDIWKKFELLPTPPLSPSRRSGLCSPSYVAVTPFSLRGDNDGGGGSFSTADQLEMVTELLGGDMVNQSFICDPD... | [
{
"source_db": "bridge",
"source_id": "4609",
"text": "MYC GENE_ENCODES_PROTEIN MYC",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "7157",
"text": "MYC PROTEIN_PHYSICALLY_INTERACTS_WITH TP53",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "... | {
"knocked_out_gene": "MYC",
"interaction_partner": "TP53",
"affected_target": "ependymal tumor",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.784499 |
co_coun_00057 | counterfactual | coding_variant | hard | 4 | If C9orf72 were knocked out, its physical interaction with CDKN2A would be lost. Which disease association of CDKN2A could therefore be indirectly affected? | C9orf72 GENE_ENCODES_PROTEIN C9orf72 -> C9orf72 PROTEIN_PHYSICALLY_INTERACTS_WITH CDKN2A -> CDKN2A GENE_ENCODES_PROTEIN CDKN2A -> CDKN2A GENE_ASSOCIATED_WITH_DISEASE mycosis fungoides | {
"steps": [
{
"hop": 1,
"source_node_id": "C9orf72",
"source_node_type": "GENE",
"source_node_label": "C9orf72",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "... | mycosis fungoides | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "C9orf72",
"source_db": "UniProt",
"payload": {
"accession": "Q96LT7",
"sequence": "MSTLCPPPSPAVAKTEIALSGKSPLLAATFAYWDNILGPRVRHIWAPKTEQVLLSDGEITFLANHTLNGEILRNAESGAIDVKFFVLSEKGVIIVSLIFDGNWNGDRSTYGLSIILPQTELSFYLPLHRVC... | [
{
"source_db": "bridge",
"source_id": "203228",
"text": "C9orf72 GENE_ENCODES_PROTEIN C9orf72",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1029",
"text": "C9orf72 PROTEIN_PHYSICALLY_INTERACTS_WITH CDKN2A",
"confidence": 0.9
},
{
"source_db": "bridge",
... | {
"knocked_out_gene": "C9orf72",
"interaction_partner": "CDKN2A",
"affected_target": "mycosis fungoides",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00058 | counterfactual | coding_variant | hard | 4 | If ACTB were knocked out, its physical interaction with MAPT would be lost. Which disease association of MAPT could therefore be indirectly affected? | ACTB GENE_ENCODES_PROTEIN ACTB -> ACTB PROTEIN_PHYSICALLY_INTERACTS_WITH MAPT -> MAPT GENE_ENCODES_PROTEIN MAPT -> MAPT GENE_ASSOCIATED_WITH_DISEASE injury | {
"steps": [
{
"hop": 1,
"source_node_id": "ACTB",
"source_node_type": "GENE",
"source_node_label": "ACTB",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "60",
... | injury | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACTB",
"source_db": "UniProt",
"payload": {
"accession": "P60709",
"sequence": "MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYV... | [
{
"source_db": "bridge",
"source_id": "60",
"text": "ACTB GENE_ENCODES_PROTEIN ACTB",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "4137",
"text": "ACTB PROTEIN_PHYSICALLY_INTERACTS_WITH MAPT",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": ... | {
"knocked_out_gene": "ACTB",
"interaction_partner": "MAPT",
"affected_target": "injury",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.647424 |
co_coun_00059 | counterfactual | coding_variant | hard | 3 | If BARD1 were knocked out, the BRCA1-BARD1-BACH1-DNA damage complex I complex would lose one of its members, indirectly affecting MSH6, another member of the same complex. Which disease association of MSH6 could therefore be indirectly affected? | BARD1 PROTEIN_MEMBER_OF_COMPLEX BRCA1-BARD1-BACH1-DNA damage complex I -> MSH6 PROTEIN_MEMBER_OF_COMPLEX BRCA1-BARD1-BACH1-DNA damage complex I -> MSH6 GENE_ASSOCIATED_WITH_DISEASE rectal neoplasm | {
"steps": [
{
"hop": 1,
"source_node_id": "BARD1",
"source_node_type": "GENE",
"source_node_label": "BARD1",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "... | rectal neoplasm | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BARD1",
"source_db": "UniProt",
"payload": {
"accession": "Q99728",
"sequence": "MPDNRQPRNRQPRIRSGNEPRSAPAMEPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQDLKINRQLDSMIQLCSKLRNLLHDNELSDLKEDKPRKSLF... | [
{
"source_db": "OmniPath",
"source_id": "CORUM:2817",
"text": "BARD1 PROTEIN_MEMBER_OF_COMPLEX BRCA1-BARD1-BACH1-DNA damage complex I",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "MSH6",
"text": "MSH6 PROTEIN_MEMBER_OF_COMPLEX BRCA1-BARD1-BACH1-DNA damage complex I",
... | {
"knocked_out_gene": "BARD1",
"disrupted_complex": "BRCA1-BARD1-BACH1-DNA damage complex I",
"complex_partner": "MSH6",
"affected_target": "rectal neoplasm",
"target_kind": "disease",
"mechanism": "complex"
} | 0.73094 |
co_coun_00060 | counterfactual | coding_variant | hard | 4 | If NF1 were knocked out, its physical interaction with APP would be lost. Which pathway of APP could therefore be indirectly affected? | NF1 GENE_ENCODES_PROTEIN NF1 -> NF1 PROTEIN_PHYSICALLY_INTERACTS_WITH APP -> APP GENE_ENCODES_PROTEIN APP -> APP GENE_PARTICIPATES_IN_PATHWAY TRAF6 mediated NF-kB activation | {
"steps": [
{
"hop": 1,
"source_node_id": "NF1",
"source_node_type": "GENE",
"source_node_label": "NF1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "4763",
... | TRAF6 mediated NF-kB activation | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NF1",
"source_db": "UniProt",
"payload": {
"accession": "P21359",
"sequence": "MAAHRPVEWVQAVVSRFDEQLPIKTGQQNTHTKVSTEHNKECLINISKYKFSLVISGLTTILKNVNNMRIFGEAAEKNLYLSQLIILDTLEKCLAGQPKDTMRLDETMLVKQLLPEICHFLHTCREGNQHAAELR... | [
{
"source_db": "bridge",
"source_id": "4763",
"text": "NF1 GENE_ENCODES_PROTEIN NF1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "351",
"text": "NF1 PROTEIN_PHYSICALLY_INTERACTS_WITH APP",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "AP... | {
"knocked_out_gene": "NF1",
"interaction_partner": "APP",
"affected_target": "TRAF6 mediated NF-kB activation",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00061 | counterfactual | coding_variant | hard | 4 | If CD274 were knocked out, its physical interaction with SPOP would be lost. Which disease association of SPOP could therefore be indirectly affected? | CD274 GENE_ENCODES_PROTEIN CD274 -> CD274 PROTEIN_PHYSICALLY_INTERACTS_WITH SPOP -> SPOP GENE_ENCODES_PROTEIN SPOP -> SPOP GENE_ASSOCIATED_WITH_DISEASE colon adenocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CD274",
"source_node_type": "GENE",
"source_node_label": "CD274",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "2912... | colon adenocarcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CD274",
"source_db": "UniProt",
"payload": {
"accession": "Q9NZQ7",
"sequence": "MRIFAVFIFMTYWHLLNAFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAP... | [
{
"source_db": "bridge",
"source_id": "29126",
"text": "CD274 GENE_ENCODES_PROTEIN CD274",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "8405",
"text": "CD274 PROTEIN_PHYSICALLY_INTERACTS_WITH SPOP",
"confidence": 0.9
},
{
"source_db": "bridge",
"source... | {
"knocked_out_gene": "CD274",
"interaction_partner": "SPOP",
"affected_target": "colon adenocarcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.671777 |
co_coun_00062 | counterfactual | coding_variant | hard | 4 | If CTNNB1 were knocked out, its physical interaction with TP53 would be lost. Which disease association of TP53 could therefore be indirectly affected? | CTNNB1 GENE_ENCODES_PROTEIN CTNNB1 -> CTNNB1 PROTEIN_PHYSICALLY_INTERACTS_WITH TP53 -> TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 GENE_ASSOCIATED_WITH_DISEASE gallbladder cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "CTNNB1",
"source_node_type": "GENE",
"source_node_label": "CTNNB1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "14... | gallbladder cancer | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CTNNB1",
"source_db": "UniProt",
"payload": {
"accession": "P35222",
"sequence": "MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSLSGKGNPEEEDVDTSQVLYEWEQGFSQSFTQEQVADIDGQYAMTRAQRVRAAMFPETLDEGMQIPSTQFDAAHPTNVQRLAEPSQML... | [
{
"source_db": "bridge",
"source_id": "1499",
"text": "CTNNB1 GENE_ENCODES_PROTEIN CTNNB1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "7157",
"text": "CTNNB1 PROTEIN_PHYSICALLY_INTERACTS_WITH TP53",
"confidence": 0.9
},
{
"source_db": "bridge",
"sour... | {
"knocked_out_gene": "CTNNB1",
"interaction_partner": "TP53",
"affected_target": "gallbladder cancer",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00063 | counterfactual | coding_variant | hard | 4 | If AURKA were knocked out, its physical interaction with TP53 would be lost. Which pathway of TP53 could therefore be indirectly affected? | AURKA GENE_ENCODES_PROTEIN AURKA -> AURKA PROTEIN_PHYSICALLY_INTERACTS_WITH TP53 -> TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 GENE_PARTICIPATES_IN_PATHWAY SUMOylation of transcription factors | {
"steps": [
{
"hop": 1,
"source_node_id": "AURKA",
"source_node_type": "GENE",
"source_node_label": "AURKA",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "6790... | SUMOylation of transcription factors | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AURKA",
"source_db": "UniProt",
"payload": {
"accession": "O14965",
"sequence": "MDRSKENCISGPVKATAPVGGPKRVLVTQQFPCQNPLPVNSGQAQRVLCPSNSSQRIPLQAQKLVSSHKPVQNQKQKQLQATSVPHPVSRPLNNTQKSKQPLPSAPENNPEEELASKQKNEESKKRQWALEDF... | [
{
"source_db": "bridge",
"source_id": "6790",
"text": "AURKA GENE_ENCODES_PROTEIN AURKA",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "7157",
"text": "AURKA PROTEIN_PHYSICALLY_INTERACTS_WITH TP53",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_... | {
"knocked_out_gene": "AURKA",
"interaction_partner": "TP53",
"affected_target": "SUMOylation of transcription factors",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00064 | counterfactual | coding_variant | hard | 3 | If MTA3 were knocked out, the ACTL6A / ARID1A / ARID1B / ARID2... complex would lose one of its members, indirectly affecting CREBBP, another member of the same complex. Which disease association of CREBBP could therefore be indirectly affected? | MTA3 PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2... -> CREBBP PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2... -> CREBBP GENE_ASSOCIATED_WITH_DISEASE carcinosarcoma | {
"steps": [
{
"hop": 1,
"source_node_id": "MTA3",
"source_node_type": "GENE",
"source_node_label": "MTA3",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "Co... | carcinosarcoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MTA3",
"source_db": "UniProt",
"payload": {
"accession": "Q9BTC8",
"sequence": "MAANMYRVGDYVYFENSSSNPYLIRRIEELNKTASGNVEAKVVCFYRRRDISNTLIMLADKHAKEIEEESETTVEADLTDKQKHQLKHRELFLSRQYESLPATHIRGKCSVALLNETESVLSYLDKEDTFFYSL... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC5233",
"text": "MTA3 PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2...",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "CREBBP",
"text": "CREBBP PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2..."... | {
"knocked_out_gene": "MTA3",
"disrupted_complex": "ACTL6A / ARID1A / ARID1B / ARID2...",
"complex_partner": "CREBBP",
"affected_target": "carcinosarcoma",
"target_kind": "disease",
"mechanism": "complex"
} | 0.652448 |
co_coun_00065 | counterfactual | coding_variant | hard | 4 | If AKT1 were knocked out, its physical interaction with FUS would be lost. Which disease association of FUS could therefore be indirectly affected? | AKT1 GENE_ENCODES_PROTEIN AKT1 -> AKT1 PROTEIN_PHYSICALLY_INTERACTS_WITH FUS -> FUS GENE_ENCODES_PROTEIN FUS -> FUS GENE_ASSOCIATED_WITH_DISEASE breast carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "AKT1",
"source_node_type": "GENE",
"source_node_label": "AKT1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "207",
... | breast carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AKT1",
"source_db": "UniProt",
"payload": {
"accession": "P31749",
"sequence": "MSDVAIVKEGWLHKRGEYIKTWRPRYFLLKNDGTFIGYKERPQDVDQREAPLNNFSVAQCQLMKTERPRPNTFIIRCLQWTTVIERTFHVETPEEREEWTTAIQTVADGLKKQEEEEMDFRSGSPSDNSGAEEM... | [
{
"source_db": "bridge",
"source_id": "207",
"text": "AKT1 GENE_ENCODES_PROTEIN AKT1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "2521",
"text": "AKT1 PROTEIN_PHYSICALLY_INTERACTS_WITH FUS",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": ... | {
"knocked_out_gene": "AKT1",
"interaction_partner": "FUS",
"affected_target": "breast carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.672944 |
co_coun_00066 | counterfactual | coding_variant | hard | 4 | If BIN1 were knocked out, its physical interaction with MYC would be lost. Which disease association of MYC could therefore be indirectly affected? | BIN1 GENE_ENCODES_PROTEIN BIN1 -> BIN1 PROTEIN_PHYSICALLY_INTERACTS_WITH MYC -> MYC GENE_ENCODES_PROTEIN MYC -> MYC GENE_ASSOCIATED_WITH_DISEASE renal osteodystrophy | {
"steps": [
{
"hop": 1,
"source_node_id": "BIN1",
"source_node_type": "GENE",
"source_node_label": "BIN1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "274",
... | renal osteodystrophy | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BIN1",
"source_db": "UniProt",
"payload": {
"accession": "O00499",
"sequence": "MAEMGSKGVTAGKIASNVQKKLTRAQEKVLQKLGKADETKDEQFEQCVQNFNKQLTEGTRLQKDLRTYLASVKAMHEASKKLNECLQEVYEPDWPGRDEANKIAENNDLLWMDYHQKLVDQALLTMDTYLGQFP... | [
{
"source_db": "bridge",
"source_id": "274",
"text": "BIN1 GENE_ENCODES_PROTEIN BIN1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "4609",
"text": "BIN1 PROTEIN_PHYSICALLY_INTERACTS_WITH MYC",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": ... | {
"knocked_out_gene": "BIN1",
"interaction_partner": "MYC",
"affected_target": "renal osteodystrophy",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.649005 |
co_coun_00067 | counterfactual | coding_variant | hard | 4 | If APH1B were knocked out, its physical interaction with PSEN1 would be lost. Which disease association of PSEN1 could therefore be indirectly affected? | APH1B GENE_ENCODES_PROTEIN APH1B -> APH1B PROTEIN_PHYSICALLY_INTERACTS_WITH PSEN1 -> PSEN1 GENE_ENCODES_PROTEIN PSEN1 -> PSEN1 GENE_ASSOCIATED_WITH_DISEASE dilated cardiomyopathy 1U | {
"steps": [
{
"hop": 1,
"source_node_id": "APH1B",
"source_node_type": "GENE",
"source_node_label": "APH1B",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "8346... | dilated cardiomyopathy 1U | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APH1B",
"source_db": "UniProt",
"payload": {
"accession": "Q8WW43",
"sequence": "MTAAVFFGCAFIAFGPALALYVFTIATEPLRIIFLIAGAFFWLVSLLISSLVWFMARVIIDNKDGPTQKYLLIFGAFVSVYIQEMFRFAYYKLLKKASEGLKSINPGETAPSMRLLAYVSGLGFGIMSGVFSF... | [
{
"source_db": "bridge",
"source_id": "83464",
"text": "APH1B GENE_ENCODES_PROTEIN APH1B",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "5663",
"text": "APH1B PROTEIN_PHYSICALLY_INTERACTS_WITH PSEN1",
"confidence": 0.9
},
{
"source_db": "bridge",
"sourc... | {
"knocked_out_gene": "APH1B",
"interaction_partner": "PSEN1",
"affected_target": "dilated cardiomyopathy 1U",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.820928 |
co_coun_00068 | counterfactual | coding_variant | hard | 4 | If PARK7 were knocked out, its physical interaction with TP53 would be lost. Which pathway of TP53 could therefore be indirectly affected? | PARK7 GENE_ENCODES_PROTEIN PARK7 -> PARK7 PROTEIN_PHYSICALLY_INTERACTS_WITH TP53 -> TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 GENE_PARTICIPATES_IN_PATHWAY Autodegradation of the E3 ubiquitin ligase COP1 | {
"steps": [
{
"hop": 1,
"source_node_id": "PARK7",
"source_node_type": "GENE",
"source_node_label": "PARK7",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "1131... | Autodegradation of the E3 ubiquitin ligase COP1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PARK7",
"source_db": "UniProt",
"payload": {
"accession": "Q99497",
"sequence": "MASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLEDAKKEGPYDVVVLPGGNLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGFGSKVTTHPLAKDKM... | [
{
"source_db": "bridge",
"source_id": "11315",
"text": "PARK7 GENE_ENCODES_PROTEIN PARK7",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "7157",
"text": "PARK7 PROTEIN_PHYSICALLY_INTERACTS_WITH TP53",
"confidence": 0.9
},
{
"source_db": "bridge",
"source... | {
"knocked_out_gene": "PARK7",
"interaction_partner": "TP53",
"affected_target": "Autodegradation of the E3 ubiquitin ligase COP1",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00069 | counterfactual | coding_variant | hard | 4 | If CD2AP were knocked out, its physical interaction with EGFR would be lost. Which disease association of EGFR could therefore be indirectly affected? | CD2AP GENE_ENCODES_PROTEIN CD2AP -> CD2AP PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR -> EGFR GENE_ENCODES_PROTEIN EGFR -> EGFR GENE_ASSOCIATED_WITH_DISEASE breast cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "CD2AP",
"source_node_type": "GENE",
"source_node_label": "CD2AP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "2360... | breast cancer | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CD2AP",
"source_db": "UniProt",
"payload": {
"accession": "Q9Y5K6",
"sequence": "MVDYIVEYDYDAVHDDELTIRVGEIIRNVKKLQEEGWLEGELNGRRGMFPDNFVKEIKRETEFKDDSLPIKRERHGNVASLVQRISTYGLPAGGIQPHPQTKNIKKKTKKRQCKVLFEYIPQNEDELELKVGD... | [
{
"source_db": "bridge",
"source_id": "23607",
"text": "CD2AP GENE_ENCODES_PROTEIN CD2AP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1956",
"text": "CD2AP PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source... | {
"knocked_out_gene": "CD2AP",
"interaction_partner": "EGFR",
"affected_target": "breast cancer",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00070 | counterfactual | coding_variant | hard | 4 | If EGFR were knocked out, its physical interaction with JAK2 would be lost. Which disease association of JAK2 could therefore be indirectly affected? | EGFR GENE_ENCODES_PROTEIN EGFR -> EGFR PROTEIN_PHYSICALLY_INTERACTS_WITH JAK2 -> JAK2 GENE_ENCODES_PROTEIN JAK2 -> JAK2 GENE_ASSOCIATED_WITH_DISEASE cellulitis | {
"steps": [
{
"hop": 1,
"source_node_id": "EGFR",
"source_node_type": "GENE",
"source_node_label": "EGFR",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "1956",... | cellulitis | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "EGFR",
"source_db": "UniProt",
"payload": {
"accession": "P00533",
"sequence": "MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQIIRGNMYYENSYALAVLSNYDANKTGLKE... | [
{
"source_db": "bridge",
"source_id": "1956",
"text": "EGFR GENE_ENCODES_PROTEIN EGFR",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "3717",
"text": "EGFR PROTEIN_PHYSICALLY_INTERACTS_WITH JAK2",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"knocked_out_gene": "EGFR",
"interaction_partner": "JAK2",
"affected_target": "cellulitis",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.693803 |
co_coun_00071 | counterfactual | coding_variant | hard | 4 | If VCP were knocked out, its physical interaction with MYC would be lost. Which pathway of MYC could therefore be indirectly affected? | VCP GENE_ENCODES_PROTEIN VCP -> VCP PROTEIN_PHYSICALLY_INTERACTS_WITH MYC -> MYC GENE_ENCODES_PROTEIN MYC -> MYC GENE_PARTICIPATES_IN_PATHWAY Constitutive Signaling by NOTCH1 PEST Domain Mutants | {
"steps": [
{
"hop": 1,
"source_node_id": "VCP",
"source_node_type": "GENE",
"source_node_label": "VCP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "7415",
... | Constitutive Signaling by NOTCH1 PEST Domain Mutants | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "VCP",
"source_db": "UniProt",
"payload": {
"accession": "P55072",
"sequence": "MASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYL... | [
{
"source_db": "bridge",
"source_id": "7415",
"text": "VCP GENE_ENCODES_PROTEIN VCP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "4609",
"text": "VCP PROTEIN_PHYSICALLY_INTERACTS_WITH MYC",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "M... | {
"knocked_out_gene": "VCP",
"interaction_partner": "MYC",
"affected_target": "Constitutive Signaling by NOTCH1 PEST Domain Mutants",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00072 | counterfactual | coding_variant | hard | 3 | If PMS2 were knocked out, the ATM / BLM / BRCA1 / EXO1... complex would lose one of its members, indirectly affecting ATM, another member of the same complex. Which disease association of ATM could therefore be indirectly affected? | PMS2 PROTEIN_MEMBER_OF_COMPLEX ATM / BLM / BRCA1 / EXO1... -> ATM PROTEIN_MEMBER_OF_COMPLEX ATM / BLM / BRCA1 / EXO1... -> ATM GENE_ASSOCIATED_WITH_DISEASE endometrioid stromal sarcoma | {
"steps": [
{
"hop": 1,
"source_node_id": "PMS2",
"source_node_type": "GENE",
"source_node_label": "PMS2",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "Co... | endometrioid stromal sarcoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PMS2",
"source_db": "UniProt",
"payload": {
"accession": "P54278",
"sequence": "MERAESSSTEPAKAIKPIDRKSVHQICSGQVVLSLSTAVKELVENSLDAGATNIDLKLKDYGVDLIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCALSDVTISTCHASAKVGTR... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC9050",
"text": "PMS2 PROTEIN_MEMBER_OF_COMPLEX ATM / BLM / BRCA1 / EXO1...",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "ATM",
"text": "ATM PROTEIN_MEMBER_OF_COMPLEX ATM / BLM / BRCA1 / EXO1...",
"confidence": 1
... | {
"knocked_out_gene": "PMS2",
"disrupted_complex": "ATM / BLM / BRCA1 / EXO1...",
"complex_partner": "ATM",
"affected_target": "endometrioid stromal sarcoma",
"target_kind": "disease",
"mechanism": "complex"
} | 0.654467 |
co_coun_00073 | counterfactual | coding_variant | hard | 4 | If CASP2 were knocked out, its physical interaction with BCL2 would be lost. Which disease association of BCL2 could therefore be indirectly affected? | CASP2 GENE_ENCODES_PROTEIN CASP2 -> CASP2 PROTEIN_PHYSICALLY_INTERACTS_WITH BCL2 -> BCL2 GENE_ENCODES_PROTEIN BCL2 -> BCL2 GENE_ASSOCIATED_WITH_DISEASE epidermoid cysts | {
"steps": [
{
"hop": 1,
"source_node_id": "CASP2",
"source_node_type": "GENE",
"source_node_label": "CASP2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "835"... | epidermoid cysts | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CASP2",
"source_db": "UniProt",
"payload": {
"accession": "P42575",
"sequence": "MAAPSAGSWSTFQHKELMAADRGRRILGVCGMHPHHQETLKKNRVVLAKQLLLSELLEHLLEKDIITLEMRELIQAKVGSFSQNVELLNLLPKRGPQAFDAFCEALRETKQGHLEDMLLTTLSGLQHVLPPLS... | [
{
"source_db": "bridge",
"source_id": "835",
"text": "CASP2 GENE_ENCODES_PROTEIN CASP2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "596",
"text": "CASP2 PROTEIN_PHYSICALLY_INTERACTS_WITH BCL2",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id... | {
"knocked_out_gene": "CASP2",
"interaction_partner": "BCL2",
"affected_target": "epidermoid cysts",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.648722 |
co_coun_00074 | counterfactual | coding_variant | medium | 3 | If ESR1 were knocked out, the ACTL6A / ARID1A / ARID1B / ARID2... complex would lose one of its members, indirectly affecting MTA3, another member of the same complex. Which pathway of MTA3 could therefore be indirectly affected? | ESR1 PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2... -> MTA3 PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2... -> MTA3 GENE_PARTICIPATES_IN_PATHWAY Potential therapeutics for SARS | {
"steps": [
{
"hop": 1,
"source_node_id": "ESR1",
"source_node_type": "GENE",
"source_node_label": "ESR1",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "Co... | Potential therapeutics for SARS | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ESR1",
"source_db": "UniProt",
"payload": {
"accession": "P03372",
"sequence": "MTMTLHTKASGMALLHQIQGNELEPLNRPQLKIPLERPLGEVYLDSSKPAVYNYPEGAAYEFNAAAAANAQVYGQTGLPYGPGSEAAAFGSNGLGGFPPLNSVSPSPLMLLHPPPQLSPFLQPHGQQVPYYLEN... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC5233",
"text": "ESR1 PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2...",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "MTA3",
"text": "MTA3 PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2...",
... | {
"knocked_out_gene": "ESR1",
"disrupted_complex": "ACTL6A / ARID1A / ARID1B / ARID2...",
"complex_partner": "MTA3",
"affected_target": "Potential therapeutics for SARS",
"target_kind": "pathway",
"mechanism": "complex"
} | 1 |
co_coun_00075 | counterfactual | coding_variant | hard | 4 | If STK11 were knocked out, its physical interaction with PTEN would be lost. Which disease association of PTEN could therefore be indirectly affected? | STK11 GENE_ENCODES_PROTEIN STK11 -> STK11 PROTEIN_PHYSICALLY_INTERACTS_WITH PTEN -> PTEN GENE_ENCODES_PROTEIN PTEN -> PTEN GENE_ASSOCIATED_WITH_DISEASE colon adenocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "STK11",
"source_node_type": "GENE",
"source_node_label": "STK11",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "6794... | colon adenocarcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "STK11",
"source_db": "UniProt",
"payload": {
"accession": "Q15831",
"sequence": "MEVVDPQQLGMFTEGELMSVGMDTFIHRIDSTEVIYQPRRKRAKLIGKYLMGDLLGEGSYGKVKEVLDSETLCRRAVKILKKKKLRRIPNGEANVKKEIQLLRRLRHKNVIQLVDVLYNEEKQKMYMVMEYCV... | [
{
"source_db": "bridge",
"source_id": "6794",
"text": "STK11 GENE_ENCODES_PROTEIN STK11",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "5728",
"text": "STK11 PROTEIN_PHYSICALLY_INTERACTS_WITH PTEN",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_... | {
"knocked_out_gene": "STK11",
"interaction_partner": "PTEN",
"affected_target": "colon adenocarcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.673448 |
co_coun_00076 | counterfactual | coding_variant | hard | 4 | If FUS were knocked out, its physical interaction with RXRA would be lost. Which disease association of RXRA could therefore be indirectly affected? | FUS GENE_ENCODES_PROTEIN FUS -> FUS PROTEIN_PHYSICALLY_INTERACTS_WITH RXRA -> RXRA GENE_ENCODES_PROTEIN RXRA -> RXRA GENE_ASSOCIATED_WITH_DISEASE undifferentiated pleomorphic sarcoma | {
"steps": [
{
"hop": 1,
"source_node_id": "FUS",
"source_node_type": "GENE",
"source_node_label": "FUS",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "2521",
... | undifferentiated pleomorphic sarcoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "FUS",
"source_db": "UniProt",
"payload": {
"accession": "P35637",
"sequence": "MASNDYTQQATQSYGAYPTQPGQGYSQQSSQPYGQQSYSGYSQSTDTSGYGQSSYSSYGQSQNTGYGTQSTPQGYGSTGGYGSSQSSQSSYGQQSSYPGYGQQPAPSSTSGSYGSSSQSSSYGQPQSGSYSQQPS... | [
{
"source_db": "bridge",
"source_id": "2521",
"text": "FUS GENE_ENCODES_PROTEIN FUS",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "6256",
"text": "FUS PROTEIN_PHYSICALLY_INTERACTS_WITH RXRA",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "... | {
"knocked_out_gene": "FUS",
"interaction_partner": "RXRA",
"affected_target": "undifferentiated pleomorphic sarcoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670462 |
co_coun_00077 | counterfactual | coding_variant | hard | 4 | If BCL2 were knocked out, its physical interaction with BRCA1 would be lost. Which disease association of BRCA1 could therefore be indirectly affected? | BCL2 GENE_ENCODES_PROTEIN BCL2 -> BCL2 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1 -> BRCA1 GENE_ENCODES_PROTEIN BRCA1 -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE Chromosome Breaks | {
"steps": [
{
"hop": 1,
"source_node_id": "BCL2",
"source_node_type": "GENE",
"source_node_label": "BCL2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "596",
... | Chromosome Breaks | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BCL2",
"source_db": "UniProt",
"payload": {
"accession": "P10415",
"sequence": "MAHAGRTGYDNREIVMKYIHYKLSQRGYEWDAGDVGAAPPGAAPAPGIFSSQPGHTPHPAASRDPVARTSPLQTPAAPGAAAGPALSPVPPVVHLTLRQAGDDFSRRYRRDFAEMSSQLHLTPFTARGRFATVV... | [
{
"source_db": "bridge",
"source_id": "596",
"text": "BCL2 GENE_ENCODES_PROTEIN BCL2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "672",
"text": "BCL2 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "BCL2",
"interaction_partner": "BRCA1",
"affected_target": "Chromosome Breaks",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.683852 |
co_coun_00078 | counterfactual | coding_variant | hard | 4 | If CREBBP were knocked out, its physical interaction with TP53 would be lost. Which pathway of TP53 could therefore be indirectly affected? | CREBBP GENE_ENCODES_PROTEIN CREBBP -> CREBBP PROTEIN_PHYSICALLY_INTERACTS_WITH TP53 -> TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 GENE_PARTICIPATES_IN_PATHWAY TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain | {
"steps": [
{
"hop": 1,
"source_node_id": "CREBBP",
"source_node_type": "GENE",
"source_node_label": "CREBBP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "13... | TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CREBBP",
"source_db": "UniProt",
"payload": {
"accession": "Q92793",
"sequence": "MAENLLDGPPNPKRAKLSSPGFSANDSTDFGSLFDLENDLPDELIPNGGELGLLNSGNLVPDAASKHKQLSELLRGGSGSSINPGIGNVSASSPVQQGLGGQAQGQPNSANMASLSAMGKSPLSQGDSSAPS... | [
{
"source_db": "bridge",
"source_id": "1387",
"text": "CREBBP GENE_ENCODES_PROTEIN CREBBP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "7157",
"text": "CREBBP PROTEIN_PHYSICALLY_INTERACTS_WITH TP53",
"confidence": 0.9
},
{
"source_db": "bridge",
"sour... | {
"knocked_out_gene": "CREBBP",
"interaction_partner": "TP53",
"affected_target": "TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00079 | counterfactual | coding_variant | hard | 4 | If EGFR were knocked out, its physical interaction with MAPT would be lost. Which disease association of MAPT could therefore be indirectly affected? | EGFR GENE_ENCODES_PROTEIN EGFR -> EGFR PROTEIN_PHYSICALLY_INTERACTS_WITH MAPT -> MAPT GENE_ENCODES_PROTEIN MAPT -> MAPT GENE_ASSOCIATED_WITH_DISEASE hearing loss disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "EGFR",
"source_node_type": "GENE",
"source_node_label": "EGFR",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "1956",... | hearing loss disorder | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "EGFR",
"source_db": "UniProt",
"payload": {
"accession": "P00533",
"sequence": "MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQIIRGNMYYENSYALAVLSNYDANKTGLKE... | [
{
"source_db": "bridge",
"source_id": "1956",
"text": "EGFR GENE_ENCODES_PROTEIN EGFR",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "4137",
"text": "EGFR PROTEIN_PHYSICALLY_INTERACTS_WITH MAPT",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"knocked_out_gene": "EGFR",
"interaction_partner": "MAPT",
"affected_target": "hearing loss disorder",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.58805 |
co_coun_00080 | counterfactual | coding_variant | hard | 4 | If BLM were knocked out, its physical interaction with MSH6 would be lost. Which disease association of MSH6 could therefore be indirectly affected? | BLM GENE_ENCODES_PROTEIN BLM -> BLM PROTEIN_PHYSICALLY_INTERACTS_WITH MSH6 -> MSH6 GENE_ENCODES_PROTEIN MSH6 -> MSH6 GENE_ASSOCIATED_WITH_DISEASE endometrioid adenocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "BLM",
"source_node_type": "GENE",
"source_node_label": "BLM",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "641",
... | endometrioid adenocarcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BLM",
"source_db": "UniProt",
"payload": {
"accession": "P54132",
"sequence": "MAAVPQNNLQEQLERHSARTLNNKLSLSKPKFSGFTFKKKTSSDNNVSVTNVSVAKTPVLRNKDVNVTEDFSFSEPLPNTTNQQRVKDFFKNAPAGQETQRGGSKSLLPDFLQTPKEVVCTTQNTPTVKKSRDTA... | [
{
"source_db": "bridge",
"source_id": "641",
"text": "BLM GENE_ENCODES_PROTEIN BLM",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "2956",
"text": "BLM PROTEIN_PHYSICALLY_INTERACTS_WITH MSH6",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "M... | {
"knocked_out_gene": "BLM",
"interaction_partner": "MSH6",
"affected_target": "endometrioid adenocarcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.792201 |
co_coun_00081 | counterfactual | coding_variant | hard | 4 | If LRRK2 were knocked out, its physical interaction with AKT1 would be lost. Which disease association of AKT1 could therefore be indirectly affected? | LRRK2 GENE_ENCODES_PROTEIN LRRK2 -> LRRK2 PROTEIN_PHYSICALLY_INTERACTS_WITH AKT1 -> AKT1 GENE_ENCODES_PROTEIN AKT1 -> AKT1 GENE_ASSOCIATED_WITH_DISEASE lysosomal storage disease | {
"steps": [
{
"hop": 1,
"source_node_id": "LRRK2",
"source_node_type": "GENE",
"source_node_label": "LRRK2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "1208... | lysosomal storage disease | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "LRRK2",
"source_db": "UniProt",
"payload": {
"accession": "Q5S007",
"sequence": "MASGSCQGCEEDEETLKKLIVRLNNVQEGKQIETLVQILEDLLVFTYSERASKLFQGKNIHVPLLIVLDSYMRVASVQQVGWSLLCKLIEVCPGTMQSLMGPQDVGNDWEVLGVHQLILKMLTVHNASVNLSV... | [
{
"source_db": "bridge",
"source_id": "120892",
"text": "LRRK2 GENE_ENCODES_PROTEIN LRRK2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "207",
"text": "LRRK2 PROTEIN_PHYSICALLY_INTERACTS_WITH AKT1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source... | {
"knocked_out_gene": "LRRK2",
"interaction_partner": "AKT1",
"affected_target": "lysosomal storage disease",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.656401 |
co_coun_00082 | counterfactual | coding_variant | hard | 4 | If EGFR were knocked out, its physical interaction with TP53 would be lost. Which disease association of TP53 could therefore be indirectly affected? | EGFR GENE_ENCODES_PROTEIN EGFR -> EGFR PROTEIN_PHYSICALLY_INTERACTS_WITH TP53 -> TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 GENE_ASSOCIATED_WITH_DISEASE bone giant cell tumor | {
"steps": [
{
"hop": 1,
"source_node_id": "EGFR",
"source_node_type": "GENE",
"source_node_label": "EGFR",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "1956",... | bone giant cell tumor | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "EGFR",
"source_db": "UniProt",
"payload": {
"accession": "P00533",
"sequence": "MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQIIRGNMYYENSYALAVLSNYDANKTGLKE... | [
{
"source_db": "bridge",
"source_id": "1956",
"text": "EGFR GENE_ENCODES_PROTEIN EGFR",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "7157",
"text": "EGFR PROTEIN_PHYSICALLY_INTERACTS_WITH TP53",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"knocked_out_gene": "EGFR",
"interaction_partner": "TP53",
"affected_target": "bone giant cell tumor",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00083 | counterfactual | coding_variant | hard | 4 | If BRAF were knocked out, its physical interaction with NRAS would be lost. Which disease association of NRAS could therefore be indirectly affected? | BRAF GENE_ENCODES_PROTEIN BRAF -> BRAF PROTEIN_PHYSICALLY_INTERACTS_WITH NRAS -> NRAS GENE_ENCODES_PROTEIN NRAS -> NRAS GENE_ASSOCIATED_WITH_DISEASE linear nevus sebaceous syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "BRAF",
"source_node_type": "GENE",
"source_node_label": "BRAF",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "673",
... | linear nevus sebaceous syndrome | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRAF",
"source_db": "UniProt",
"payload": {
"accession": "P15056",
"sequence": "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEHIEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTVTSSSSSSLSVLPSS... | [
{
"source_db": "bridge",
"source_id": "673",
"text": "BRAF GENE_ENCODES_PROTEIN BRAF",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "4893",
"text": "BRAF PROTEIN_PHYSICALLY_INTERACTS_WITH NRAS",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "BRAF",
"interaction_partner": "NRAS",
"affected_target": "linear nevus sebaceous syndrome",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00084 | counterfactual | coding_variant | hard | 4 | If PMS2 were knocked out, its physical interaction with BRIP1 would be lost. Which disease association of BRIP1 could therefore be indirectly affected? | PMS2 GENE_ENCODES_PROTEIN PMS2 -> PMS2 PROTEIN_PHYSICALLY_INTERACTS_WITH BRIP1 -> BRIP1 GENE_ENCODES_PROTEIN BRIP1 -> BRIP1 GENE_ASSOCIATED_WITH_DISEASE metaplastic breast carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "PMS2",
"source_node_type": "GENE",
"source_node_label": "PMS2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "5395",... | metaplastic breast carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PMS2",
"source_db": "UniProt",
"payload": {
"accession": "P54278",
"sequence": "MERAESSSTEPAKAIKPIDRKSVHQICSGQVVLSLSTAVKELVENSLDAGATNIDLKLKDYGVDLIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCALSDVTISTCHASAKVGTR... | [
{
"source_db": "bridge",
"source_id": "5395",
"text": "PMS2 GENE_ENCODES_PROTEIN PMS2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "83990",
"text": "PMS2 PROTEIN_PHYSICALLY_INTERACTS_WITH BRIP1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "PMS2",
"interaction_partner": "BRIP1",
"affected_target": "metaplastic breast carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670462 |
co_coun_00085 | counterfactual | coding_variant | hard | 4 | If ABI1 were knocked out, its physical interaction with CBL would be lost. Which disease association of CBL could therefore be indirectly affected? | ABI1 GENE_ENCODES_PROTEIN ABI1 -> ABI1 PROTEIN_PHYSICALLY_INTERACTS_WITH CBL -> CBL GENE_ENCODES_PROTEIN CBL -> CBL GENE_ASSOCIATED_WITH_DISEASE epilepsy, early-onset | {
"steps": [
{
"hop": 1,
"source_node_id": "ABI1",
"source_node_type": "GENE",
"source_node_label": "ABI1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "10006"... | epilepsy, early-onset | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ABI1",
"source_db": "UniProt",
"payload": {
"accession": "Q8IZP0",
"sequence": "MAELQMLLEEEIPSGKRALIESYQNLTRVADYCENNYIQATDKRKALEETKAYTTQSLASVAYQINALANNVLQLLDIQASQLRRMESSINHISQTVDIHKEKVARREIGILTTNKNTSRTHKIIAPANMERPV... | [
{
"source_db": "bridge",
"source_id": "10006",
"text": "ABI1 GENE_ENCODES_PROTEIN ABI1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "867",
"text": "ABI1 PROTEIN_PHYSICALLY_INTERACTS_WITH CBL",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "ABI1",
"interaction_partner": "CBL",
"affected_target": "epilepsy, early-onset",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.541872 |
co_coun_00086 | counterfactual | coding_variant | hard | 4 | If VCP were knocked out, its physical interaction with TUBA4A would be lost. Which disease association of TUBA4A could therefore be indirectly affected? | VCP GENE_ENCODES_PROTEIN VCP -> VCP PROTEIN_PHYSICALLY_INTERACTS_WITH TUBA4A -> TUBA4A GENE_ENCODES_PROTEIN TUBA4A -> TUBA4A GENE_ASSOCIATED_WITH_DISEASE ST Elevation Myocardial Infarction | {
"steps": [
{
"hop": 1,
"source_node_id": "VCP",
"source_node_type": "GENE",
"source_node_label": "VCP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "7415",
... | ST Elevation Myocardial Infarction | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "VCP",
"source_db": "UniProt",
"payload": {
"accession": "P55072",
"sequence": "MASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYL... | [
{
"source_db": "bridge",
"source_id": "7415",
"text": "VCP GENE_ENCODES_PROTEIN VCP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "7277",
"text": "VCP PROTEIN_PHYSICALLY_INTERACTS_WITH TUBA4A",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "VCP",
"interaction_partner": "TUBA4A",
"affected_target": "ST Elevation Myocardial Infarction",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.696805 |
co_coun_00087 | counterfactual | coding_variant | hard | 4 | If PFN1 were knocked out, its physical interaction with PTEN would be lost. Which disease association of PTEN could therefore be indirectly affected? | PFN1 GENE_ENCODES_PROTEIN PFN1 -> PFN1 PROTEIN_PHYSICALLY_INTERACTS_WITH PTEN -> PTEN GENE_ENCODES_PROTEIN PTEN -> PTEN GENE_ASSOCIATED_WITH_DISEASE megalencephaly | {
"steps": [
{
"hop": 1,
"source_node_id": "PFN1",
"source_node_type": "GENE",
"source_node_label": "PFN1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "5216",... | megalencephaly | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PFN1",
"source_db": "UniProt",
"payload": {
"accession": "P07737",
"sequence": "MAGWNAYIDNLMADGTCQDAAIVGYKDSPSVWAAVPGKTFVNITPAEVGVLVGKDRSSFYVNGLTLGGQKCSVIRDSLLQDGEFSMDLRTKSTGGAPTFNVTVTKTDKTLVLLMGKEGVHGGLINKKCYEMASH... | [
{
"source_db": "bridge",
"source_id": "5216",
"text": "PFN1 GENE_ENCODES_PROTEIN PFN1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "5728",
"text": "PFN1 PROTEIN_PHYSICALLY_INTERACTS_WITH PTEN",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"knocked_out_gene": "PFN1",
"interaction_partner": "PTEN",
"affected_target": "megalencephaly",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.721183 |
co_coun_00088 | counterfactual | coding_variant | hard | 3 | If BRIP1 were knocked out, the BRCA1-B complex complex would lose one of its members, indirectly affecting BARD1, another member of the same complex. Which disease association of BARD1 could therefore be indirectly affected? | BRIP1 PROTEIN_MEMBER_OF_COMPLEX BRCA1-B complex -> BARD1 PROTEIN_MEMBER_OF_COMPLEX BRCA1-B complex -> BARD1 GENE_ASSOCIATED_WITH_DISEASE thyroid gland papillary carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "BRIP1",
"source_node_type": "GENE",
"source_node_label": "BRIP1",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "... | thyroid gland papillary carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRIP1",
"source_db": "UniProt",
"payload": {
"accession": "Q9BX63",
"sequence": "MSSMWSEYTIGGVKIYFPYKAYPSQLAMMNSILRGLNSKQHCLLESPTGSGKSLALLCSALAWQQSLSGKPADEGVSEKAEVQLSCCCACHSKDFTNNDMNQGTSRHFNYPSTPPSERNGTSSTCQDSPEKTT... | [
{
"source_db": "OmniPath",
"source_id": "SIGNOR:SIGNOR-C298",
"text": "BRIP1 PROTEIN_MEMBER_OF_COMPLEX BRCA1-B complex",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "BARD1",
"text": "BARD1 PROTEIN_MEMBER_OF_COMPLEX BRCA1-B complex",
"confidence": 1
},
{
"so... | {
"knocked_out_gene": "BRIP1",
"disrupted_complex": "BRCA1-B complex",
"complex_partner": "BARD1",
"affected_target": "thyroid gland papillary carcinoma",
"target_kind": "disease",
"mechanism": "complex"
} | 0.652737 |
co_coun_00089 | counterfactual | coding_variant | hard | 4 | If CDK1 were knocked out, its physical interaction with TP53 would be lost. Which disease association of TP53 could therefore be indirectly affected? | CDK1 GENE_ENCODES_PROTEIN CDK1 -> CDK1 PROTEIN_PHYSICALLY_INTERACTS_WITH TP53 -> TP53 GENE_ENCODES_PROTEIN TP53 -> TP53 GENE_ASSOCIATED_WITH_DISEASE rectal carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CDK1",
"source_node_type": "GENE",
"source_node_label": "CDK1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "983",
... | rectal carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDK1",
"source_db": "UniProt",
"payload": {
"accession": "P06493",
"sequence": "MEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLLKELRHPNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKSYLYQILQGIVFCHSRRVLHRDLKPQNL... | [
{
"source_db": "bridge",
"source_id": "983",
"text": "CDK1 GENE_ENCODES_PROTEIN CDK1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "7157",
"text": "CDK1 PROTEIN_PHYSICALLY_INTERACTS_WITH TP53",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "CDK1",
"interaction_partner": "TP53",
"affected_target": "rectal carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.723445 |
co_coun_00090 | counterfactual | coding_variant | hard | 4 | If BRCA2 were knocked out, its physical interaction with CCND1 would be lost. Which disease association of CCND1 could therefore be indirectly affected? | BRCA2 GENE_ENCODES_PROTEIN BRCA2 -> BRCA2 PROTEIN_PHYSICALLY_INTERACTS_WITH CCND1 -> CCND1 GENE_ENCODES_PROTEIN CCND1 -> CCND1 GENE_ASSOCIATED_WITH_DISEASE idiopathic pulmonary fibrosis | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA2",
"source_node_type": "GENE",
"source_node_label": "BRCA2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "675"... | idiopathic pulmonary fibrosis | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA2",
"source_db": "UniProt",
"payload": {
"accession": "P51587",
"sequence": "MPIGSKERPTFFEIFKTRCNKADLGPISLNWFEELSSEAPPYNSEPAEESEHKNNNYEPNLFKTPQRKPSYNQLASTPIIFKEQGLTLPLYQSPVKELDKFKLDLGRNVPNSRHKSLRTVKTKMDQADDVSCP... | [
{
"source_db": "bridge",
"source_id": "675",
"text": "BRCA2 GENE_ENCODES_PROTEIN BRCA2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "595",
"text": "BRCA2 PROTEIN_PHYSICALLY_INTERACTS_WITH CCND1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "BRCA2",
"interaction_partner": "CCND1",
"affected_target": "idiopathic pulmonary fibrosis",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.606511 |
co_coun_00091 | counterfactual | coding_variant | hard | 3 | If MSH6 were knocked out, the BASC complex (BRCA1-associated genome surveillance complex) complex would lose one of its members, indirectly affecting BLM, another member of the same complex. Which disease association of BLM could therefore be indirectly affected? | MSH6 PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-associated genome surveillance complex) -> BLM PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-associated genome surveillance complex) -> BLM GENE_ASSOCIATED_WITH_DISEASE ependymoma | {
"steps": [
{
"hop": 1,
"source_node_id": "MSH6",
"source_node_type": "GENE",
"source_node_label": "MSH6",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "CO... | ependymoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH6",
"source_db": "UniProt",
"payload": {
"accession": "P52701",
"sequence": "MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFF... | [
{
"source_db": "OmniPath",
"source_id": "CORUM:433",
"text": "MSH6 PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-associated genome surveillance complex)",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "BLM",
"text": "BLM PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-asso... | {
"knocked_out_gene": "MSH6",
"disrupted_complex": "BASC complex (BRCA1-associated genome surveillance complex)",
"complex_partner": "BLM",
"affected_target": "ependymoma",
"target_kind": "disease",
"mechanism": "complex"
} | 0.569586 |
co_coun_00092 | counterfactual | coding_variant | hard | 4 | If BRAF were knocked out, its physical interaction with MAPK1 would be lost. Which pathway of MAPK1 could therefore be indirectly affected? | BRAF GENE_ENCODES_PROTEIN BRAF -> BRAF PROTEIN_PHYSICALLY_INTERACTS_WITH MAPK1 -> MAPK1 GENE_ENCODES_PROTEIN MAPK1 -> MAPK1 GENE_PARTICIPATES_IN_PATHWAY Gastrin-CREB signalling pathway via PKC and MAPK | {
"steps": [
{
"hop": 1,
"source_node_id": "BRAF",
"source_node_type": "GENE",
"source_node_label": "BRAF",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "673",
... | Gastrin-CREB signalling pathway via PKC and MAPK | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRAF",
"source_db": "UniProt",
"payload": {
"accession": "P15056",
"sequence": "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEHIEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTVTSSSSSSLSVLPSS... | [
{
"source_db": "bridge",
"source_id": "673",
"text": "BRAF GENE_ENCODES_PROTEIN BRAF",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "5594",
"text": "BRAF PROTEIN_PHYSICALLY_INTERACTS_WITH MAPK1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"knocked_out_gene": "BRAF",
"interaction_partner": "MAPK1",
"affected_target": "Gastrin-CREB signalling pathway via PKC and MAPK",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00093 | counterfactual | coding_variant | hard | 4 | If AXL were knocked out, its physical interaction with EGFR would be lost. Which disease association of EGFR could therefore be indirectly affected? | AXL GENE_ENCODES_PROTEIN AXL -> AXL PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR -> EGFR GENE_ENCODES_PROTEIN EGFR -> EGFR GENE_ASSOCIATED_WITH_DISEASE head and neck cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "AXL",
"source_node_type": "GENE",
"source_node_label": "AXL",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "558",
... | head and neck cancer | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AXL",
"source_db": "UniProt",
"payload": {
"accession": "P30530",
"sequence": "MAWRCPRMGRVPLAWCLALCGWACMAPRGTQAEESPFVGNPGNITGARGLTGTLRCQLQVQGEPPEVHWLRDGQILELADSTQTQVPLGEDEQDDWIVVSQLRITSLQLSDTGQYQCLVFLGHQTFVSQPGYVGL... | [
{
"source_db": "bridge",
"source_id": "558",
"text": "AXL GENE_ENCODES_PROTEIN AXL",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1956",
"text": "AXL PROTEIN_PHYSICALLY_INTERACTS_WITH EGFR",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "E... | {
"knocked_out_gene": "AXL",
"interaction_partner": "EGFR",
"affected_target": "head and neck cancer",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.820613 |
co_coun_00094 | counterfactual | coding_variant | hard | 3 | If BARD1 were knocked out, the BRCA1-BARD1 complex complex would lose one of its members, indirectly affecting BRCA1, another member of the same complex. Which disease association of BRCA1 could therefore be indirectly affected? | BARD1 PROTEIN_MEMBER_OF_COMPLEX BRCA1-BARD1 complex -> BRCA1 PROTEIN_MEMBER_OF_COMPLEX BRCA1-BARD1 complex -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE alveolar rhabdomyosarcoma | {
"steps": [
{
"hop": 1,
"source_node_id": "BARD1",
"source_node_type": "GENE",
"source_node_label": "BARD1",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "... | alveolar rhabdomyosarcoma | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BARD1",
"source_db": "UniProt",
"payload": {
"accession": "Q99728",
"sequence": "MPDNRQPRNRQPRIRSGNEPRSAPAMEPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQDLKINRQLDSMIQLCSKLRNLLHDNELSDLKEDKPRKSLF... | [
{
"source_db": "OmniPath",
"source_id": "CORUM:201",
"text": "BARD1 PROTEIN_MEMBER_OF_COMPLEX BRCA1-BARD1 complex",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "BRCA1",
"text": "BRCA1 PROTEIN_MEMBER_OF_COMPLEX BRCA1-BARD1 complex",
"confidence": 1
},
{
"sou... | {
"knocked_out_gene": "BARD1",
"disrupted_complex": "BRCA1-BARD1 complex",
"complex_partner": "BRCA1",
"affected_target": "alveolar rhabdomyosarcoma",
"target_kind": "disease",
"mechanism": "complex"
} | 0.652013 |
co_coun_00095 | counterfactual | coding_variant | hard | 4 | If AR were knocked out, its physical interaction with CREBBP would be lost. Which pathway of CREBBP could therefore be indirectly affected? | AR GENE_ENCODES_PROTEIN AR -> AR PROTEIN_PHYSICALLY_INTERACTS_WITH CREBBP -> CREBBP GENE_ENCODES_PROTEIN CREBBP -> CREBBP GENE_PARTICIPATES_IN_PATHWAY Nuclear events mediated by NFE2L2 | {
"steps": [
{
"hop": 1,
"source_node_id": "AR",
"source_node_type": "GENE",
"source_node_label": "AR",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "367",
... | Nuclear events mediated by NFE2L2 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AR",
"source_db": "UniProt",
"payload": {
"accession": "P10275",
"sequence": "MEVQLGLGRVYPRPPSKTYRGAFQNLFQSVREVIQNPGPRHPEAASAAPPGASLLLLQQQQQQQQQQQQQQQQQQQQQQQETSPRQQQQQQGEDGSPQAHRRGPTGYLVLDEEQQPSQPQSALECHPERGCVPEPG... | [
{
"source_db": "bridge",
"source_id": "367",
"text": "AR GENE_ENCODES_PROTEIN AR",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "1387",
"text": "AR PROTEIN_PHYSICALLY_INTERACTS_WITH CREBBP",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "CR... | {
"knocked_out_gene": "AR",
"interaction_partner": "CREBBP",
"affected_target": "Nuclear events mediated by NFE2L2",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00096 | counterfactual | coding_variant | hard | 4 | If VCP were knocked out, its physical interaction with CHEK2 would be lost. Which pathway of CHEK2 could therefore be indirectly affected? | VCP GENE_ENCODES_PROTEIN VCP -> VCP PROTEIN_PHYSICALLY_INTERACTS_WITH CHEK2 -> CHEK2 GENE_ENCODES_PROTEIN CHEK2 -> CHEK2 GENE_PARTICIPATES_IN_PATHWAY Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex | {
"steps": [
{
"hop": 1,
"source_node_id": "VCP",
"source_node_type": "GENE",
"source_node_label": "VCP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "7415",
... | Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "VCP",
"source_db": "UniProt",
"payload": {
"accession": "P55072",
"sequence": "MASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYL... | [
{
"source_db": "bridge",
"source_id": "7415",
"text": "VCP GENE_ENCODES_PROTEIN VCP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "11200",
"text": "VCP PROTEIN_PHYSICALLY_INTERACTS_WITH CHEK2",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "VCP",
"interaction_partner": "CHEK2",
"affected_target": "Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00097 | counterfactual | coding_variant | hard | 3 | If ATM were knocked out, the BASC complex (BRCA1-associated genome surveillance complex) complex would lose one of its members, indirectly affecting BLM, another member of the same complex. Which disease association of BLM could therefore be indirectly affected? | ATM PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-associated genome surveillance complex) -> BLM PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-associated genome surveillance complex) -> BLM GENE_ASSOCIATED_WITH_DISEASE acute myeloid leukemia | {
"steps": [
{
"hop": 1,
"source_node_id": "ATM",
"source_node_type": "GENE",
"source_node_label": "ATM",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "CORU... | acute myeloid leukemia | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ATM",
"source_db": "UniProt",
"payload": {
"accession": "Q13315",
"sequence": "MSLVLNDLLICCRQLEHDRATERKKEVEKFKRLIRDPETIKHLDRHSDSKQGKYLNWDAVFRFLQKYIQKETECLRIAKPNVSASTQASRQKKMQEISSLVKYFIKCANRRAPRLKCQELLNYIMDTVKDSSNGA... | [
{
"source_db": "OmniPath",
"source_id": "CORUM:433",
"text": "ATM PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-associated genome surveillance complex)",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "BLM",
"text": "BLM PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-assoc... | {
"knocked_out_gene": "ATM",
"disrupted_complex": "BASC complex (BRCA1-associated genome surveillance complex)",
"complex_partner": "BLM",
"affected_target": "acute myeloid leukemia",
"target_kind": "disease",
"mechanism": "complex"
} | 0.761403 |
co_coun_00098 | counterfactual | coding_variant | hard | 4 | If CD44 were knocked out, its physical interaction with FGFR1 would be lost. Which disease association of FGFR1 could therefore be indirectly affected? | CD44 GENE_ENCODES_PROTEIN CD44 -> CD44 PROTEIN_PHYSICALLY_INTERACTS_WITH FGFR1 -> FGFR1 GENE_ENCODES_PROTEIN FGFR1 -> FGFR1 GENE_ASSOCIATED_WITH_DISEASE neuroendocrine carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CD44",
"source_node_type": "GENE",
"source_node_label": "CD44",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "960",
... | neuroendocrine carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CD44",
"source_db": "UniProt",
"payload": {
"accession": "P16070",
"sequence": "MDKFWWHAAWGLCLVPLSLAQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFETCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTD... | [
{
"source_db": "bridge",
"source_id": "960",
"text": "CD44 GENE_ENCODES_PROTEIN CD44",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "2260",
"text": "CD44 PROTEIN_PHYSICALLY_INTERACTS_WITH FGFR1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id"... | {
"knocked_out_gene": "CD44",
"interaction_partner": "FGFR1",
"affected_target": "neuroendocrine carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.707032 |
co_coun_00099 | counterfactual | coding_variant | hard | 3 | If CREBBP were knocked out, the ACTL6A / ARID1A / ARID1B / ARID2... complex would lose one of its members, indirectly affecting MYC, another member of the same complex. Which disease association of MYC could therefore be indirectly affected? | CREBBP PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2... -> MYC PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2... -> MYC GENE_ASSOCIATED_WITH_DISEASE allergic rhinitis | {
"steps": [
{
"hop": 1,
"source_node_id": "CREBBP",
"source_node_type": "GENE",
"source_node_label": "CREBBP",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id":... | allergic rhinitis | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CREBBP",
"source_db": "UniProt",
"payload": {
"accession": "Q92793",
"sequence": "MAENLLDGPPNPKRAKLSSPGFSANDSTDFGSLFDLENDLPDELIPNGGELGLLNSGNLVPDAASKHKQLSELLRGGSGSSINPGIGNVSASSPVQQGLGGQAQGQPNSANMASLSAMGKSPLSQGDSSAPS... | [
{
"source_db": "OmniPath",
"source_id": "Compleat:HC5233",
"text": "CREBBP PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2...",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "MYC",
"text": "MYC PROTEIN_MEMBER_OF_COMPLEX ACTL6A / ARID1A / ARID1B / ARID2...",
... | {
"knocked_out_gene": "CREBBP",
"disrupted_complex": "ACTL6A / ARID1A / ARID1B / ARID2...",
"complex_partner": "MYC",
"affected_target": "allergic rhinitis",
"target_kind": "disease",
"mechanism": "complex"
} | 0.753375 |
co_coun_00100 | counterfactual | coding_variant | hard | 4 | If CREBBP were knocked out, its physical interaction with AKT1 would be lost. Which disease association of AKT1 could therefore be indirectly affected? | CREBBP GENE_ENCODES_PROTEIN CREBBP -> CREBBP PROTEIN_PHYSICALLY_INTERACTS_WITH AKT1 -> AKT1 GENE_ENCODES_PROTEIN AKT1 -> AKT1 GENE_ASSOCIATED_WITH_DISEASE sinonasal undifferentiated carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CREBBP",
"source_node_type": "GENE",
"source_node_label": "CREBBP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "13... | sinonasal undifferentiated carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CREBBP",
"source_db": "UniProt",
"payload": {
"accession": "Q92793",
"sequence": "MAENLLDGPPNPKRAKLSSPGFSANDSTDFGSLFDLENDLPDELIPNGGELGLLNSGNLVPDAASKHKQLSELLRGGSGSSINPGIGNVSASSPVQQGLGGQAQGQPNSANMASLSAMGKSPLSQGDSSAPS... | [
{
"source_db": "bridge",
"source_id": "1387",
"text": "CREBBP GENE_ENCODES_PROTEIN CREBBP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "207",
"text": "CREBBP PROTEIN_PHYSICALLY_INTERACTS_WITH AKT1",
"confidence": 0.9
},
{
"source_db": "bridge",
"sourc... | {
"knocked_out_gene": "CREBBP",
"interaction_partner": "AKT1",
"affected_target": "sinonasal undifferentiated carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.605831 |
co_coun_00101 | counterfactual | coding_variant | hard | 4 | If KRAS were knocked out, its physical interaction with PIK3CA would be lost. Which disease association of PIK3CA could therefore be indirectly affected? | KRAS GENE_ENCODES_PROTEIN KRAS -> KRAS PROTEIN_PHYSICALLY_INTERACTS_WITH PIK3CA -> PIK3CA GENE_ENCODES_PROTEIN PIK3CA -> PIK3CA GENE_ASSOCIATED_WITH_DISEASE astrocytoma (excluding glioblastoma) | {
"steps": [
{
"hop": 1,
"source_node_id": "KRAS",
"source_node_type": "GENE",
"source_node_label": "KRAS",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "3845",... | astrocytoma (excluding glioblastoma) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KRAS",
"source_db": "UniProt",
"payload": {
"accession": "P01116",
"sequence": "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLA... | [
{
"source_db": "bridge",
"source_id": "3845",
"text": "KRAS GENE_ENCODES_PROTEIN KRAS",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "5290",
"text": "KRAS PROTEIN_PHYSICALLY_INTERACTS_WITH PIK3CA",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_i... | {
"knocked_out_gene": "KRAS",
"interaction_partner": "PIK3CA",
"affected_target": "astrocytoma (excluding glioblastoma)",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.673913 |
co_coun_00102 | counterfactual | coding_variant | hard | 4 | If APP were knocked out, its physical interaction with KRAS would be lost. Which disease association of KRAS could therefore be indirectly affected? | APP GENE_ENCODES_PROTEIN APP -> APP PROTEIN_PHYSICALLY_INTERACTS_WITH KRAS -> KRAS GENE_ENCODES_PROTEIN KRAS -> KRAS GENE_ASSOCIATED_WITH_DISEASE Borderline Ovarian Mucinous Tumor | {
"steps": [
{
"hop": 1,
"source_node_id": "APP",
"source_node_type": "GENE",
"source_node_label": "APP",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "351",
... | Borderline Ovarian Mucinous Tumor | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APP",
"source_db": "UniProt",
"payload": {
"accession": "P05067",
"sequence": "MLPGLALLLLAAWTARALEVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGILQYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKF... | [
{
"source_db": "bridge",
"source_id": "351",
"text": "APP GENE_ENCODES_PROTEIN APP",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "3845",
"text": "APP PROTEIN_PHYSICALLY_INTERACTS_WITH KRAS",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": "K... | {
"knocked_out_gene": "APP",
"interaction_partner": "KRAS",
"affected_target": "Borderline Ovarian Mucinous Tumor",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.721185 |
co_coun_00103 | counterfactual | coding_variant | hard | 4 | If LRRK2 were knocked out, its physical interaction with AKT1 would be lost. Which pathway of AKT1 could therefore be indirectly affected? | LRRK2 GENE_ENCODES_PROTEIN LRRK2 -> LRRK2 PROTEIN_PHYSICALLY_INTERACTS_WITH AKT1 -> AKT1 GENE_ENCODES_PROTEIN AKT1 -> AKT1 GENE_PARTICIPATES_IN_PATHWAY Activation of BAD and translocation to mitochondria | {
"steps": [
{
"hop": 1,
"source_node_id": "LRRK2",
"source_node_type": "GENE",
"source_node_label": "LRRK2",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "1208... | Activation of BAD and translocation to mitochondria | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "LRRK2",
"source_db": "UniProt",
"payload": {
"accession": "Q5S007",
"sequence": "MASGSCQGCEEDEETLKKLIVRLNNVQEGKQIETLVQILEDLLVFTYSERASKLFQGKNIHVPLLIVLDSYMRVASVQQVGWSLLCKLIEVCPGTMQSLMGPQDVGNDWEVLGVHQLILKMLTVHNASVNLSV... | [
{
"source_db": "bridge",
"source_id": "120892",
"text": "LRRK2 GENE_ENCODES_PROTEIN LRRK2",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "207",
"text": "LRRK2 PROTEIN_PHYSICALLY_INTERACTS_WITH AKT1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source... | {
"knocked_out_gene": "LRRK2",
"interaction_partner": "AKT1",
"affected_target": "Activation of BAD and translocation to mitochondria ",
"target_kind": "pathway",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00104 | counterfactual | coding_variant | hard | 4 | If CDK1 were knocked out, its physical interaction with BRCA1 would be lost. Which disease association of BRCA1 could therefore be indirectly affected? | CDK1 GENE_ENCODES_PROTEIN CDK1 -> CDK1 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1 -> BRCA1 GENE_ENCODES_PROTEIN BRCA1 -> BRCA1 GENE_ASSOCIATED_WITH_DISEASE adenoid cystic carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CDK1",
"source_node_type": "GENE",
"source_node_label": "CDK1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "983",
... | adenoid cystic carcinoma | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDK1",
"source_db": "UniProt",
"payload": {
"accession": "P06493",
"sequence": "MEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLLKELRHPNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKSYLYQILQGIVFCHSRRVLHRDLKPQNL... | [
{
"source_db": "bridge",
"source_id": "983",
"text": "CDK1 GENE_ENCODES_PROTEIN CDK1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "672",
"text": "CDK1 PROTEIN_PHYSICALLY_INTERACTS_WITH BRCA1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id":... | {
"knocked_out_gene": "CDK1",
"interaction_partner": "BRCA1",
"affected_target": "adenoid cystic carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.689481 |
co_coun_00105 | counterfactual | coding_variant | hard | 3 | If BRCA1 were knocked out, the BASC complex (BRCA1-associated genome surveillance complex) complex would lose one of its members, indirectly affecting ATM, another member of the same complex. Which disease association of ATM could therefore be indirectly affected? | BRCA1 PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-associated genome surveillance complex) -> ATM PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-associated genome surveillance complex) -> ATM GENE_ASSOCIATED_WITH_DISEASE combined hepatocellular carcinoma and cholangiocarcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA1",
"source_node_type": "GENE",
"source_node_label": "BRCA1",
"edge_relation": "PROTEIN_MEMBER_OF_COMPLEX",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "OmniPath",
"target_node_id": "... | combined hepatocellular carcinoma and cholangiocarcinoma | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA1",
"source_db": "UniProt",
"payload": {
"accession": "P38398",
"sequence": "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNR... | [
{
"source_db": "OmniPath",
"source_id": "CORUM:433",
"text": "BRCA1 PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-associated genome surveillance complex)",
"confidence": 1
},
{
"source_db": "OmniPath",
"source_id": "ATM",
"text": "ATM PROTEIN_MEMBER_OF_COMPLEX BASC complex (BRCA1-ass... | {
"knocked_out_gene": "BRCA1",
"disrupted_complex": "BASC complex (BRCA1-associated genome surveillance complex)",
"complex_partner": "ATM",
"affected_target": "combined hepatocellular carcinoma and cholangiocarcinoma",
"target_kind": "disease",
"mechanism": "complex"
} | 0.652013 |
co_coun_00106 | counterfactual | coding_variant | hard | 4 | If APC were knocked out, its physical interaction with TUBA4A would be lost. Which disease association of TUBA4A could therefore be indirectly affected? | APC GENE_ENCODES_PROTEIN APC -> APC PROTEIN_PHYSICALLY_INTERACTS_WITH TUBA4A -> TUBA4A GENE_ENCODES_PROTEIN TUBA4A -> TUBA4A GENE_ASSOCIATED_WITH_DISEASE Frontotemporal dementia and amyotrophic lateral sclerosis | {
"steps": [
{
"hop": 1,
"source_node_id": "APC",
"source_node_type": "GENE",
"source_node_label": "APC",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "324",
... | Frontotemporal dementia and amyotrophic lateral sclerosis | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APC",
"source_db": "UniProt",
"payload": {
"accession": "P25054",
"sequence": "MAAASYDQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLE... | [
{
"source_db": "bridge",
"source_id": "324",
"text": "APC GENE_ENCODES_PROTEIN APC",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "7277",
"text": "APC PROTEIN_PHYSICALLY_INTERACTS_WITH TUBA4A",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_id": ... | {
"knocked_out_gene": "APC",
"interaction_partner": "TUBA4A",
"affected_target": "Frontotemporal dementia and amyotrophic lateral sclerosis",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.924021 |
co_coun_00107 | counterfactual | coding_variant | hard | 4 | If MAPK1 were knocked out, its physical interaction with KRAS would be lost. Which disease association of KRAS could therefore be indirectly affected? | MAPK1 GENE_ENCODES_PROTEIN MAPK1 -> MAPK1 PROTEIN_PHYSICALLY_INTERACTS_WITH KRAS -> KRAS GENE_ENCODES_PROTEIN KRAS -> KRAS GENE_ASSOCIATED_WITH_DISEASE thymic carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "MAPK1",
"source_node_type": "GENE",
"source_node_label": "MAPK1",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "5594... | thymic carcinoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MAPK1",
"source_db": "UniProt",
"payload": {
"accession": "P28482",
"sequence": "MAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQI... | [
{
"source_db": "bridge",
"source_id": "5594",
"text": "MAPK1 GENE_ENCODES_PROTEIN MAPK1",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "3845",
"text": "MAPK1 PROTEIN_PHYSICALLY_INTERACTS_WITH KRAS",
"confidence": 0.9
},
{
"source_db": "bridge",
"source_... | {
"knocked_out_gene": "MAPK1",
"interaction_partner": "KRAS",
"affected_target": "thymic carcinoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.673355 |
co_coun_00108 | counterfactual | coding_variant | hard | 4 | If CAMK4 were knocked out, its physical interaction with NOTCH1 would be lost. Which disease association of NOTCH1 could therefore be indirectly affected? | CAMK4 GENE_ENCODES_PROTEIN CAMK4 -> CAMK4 PROTEIN_PHYSICALLY_INTERACTS_WITH NOTCH1 -> NOTCH1 GENE_ENCODES_PROTEIN NOTCH1 -> NOTCH1 GENE_ASSOCIATED_WITH_DISEASE salivary gland carcinoma ex pleomorphic adenoma | {
"steps": [
{
"hop": 1,
"source_node_id": "CAMK4",
"source_node_type": "GENE",
"source_node_label": "CAMK4",
"edge_relation": "GENE_ENCODES_PROTEIN",
"edge_evidence_type": "inferred",
"edge_confidence": 0.9,
"edge_source_db": "bridge",
"target_node_id": "814"... | salivary gland carcinoma ex pleomorphic adenoma | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CAMK4",
"source_db": "UniProt",
"payload": {
"accession": "Q16566",
"sequence": "MLKVTVPSCSASSCSSVTASAAPGTASLVPDYWIDGSNRDALSDFFEVESELGRGATSIVYRCKQKGTQKPYALKVLKKTVDKKIVRTEIGVLLRLSHPNIIKLKEIFETPTEISLVLELVTGGELFDRIVEK... | [
{
"source_db": "bridge",
"source_id": "814",
"text": "CAMK4 GENE_ENCODES_PROTEIN CAMK4",
"confidence": 0.9
},
{
"source_db": "BioGRID",
"source_id": "4851",
"text": "CAMK4 PROTEIN_PHYSICALLY_INTERACTS_WITH NOTCH1",
"confidence": 0.9
},
{
"source_db": "bridge",
"source... | {
"knocked_out_gene": "CAMK4",
"interaction_partner": "NOTCH1",
"affected_target": "salivary gland carcinoma ex pleomorphic adenoma",
"target_kind": "disease",
"mechanism": "pairwise"
} | 0.670462 |
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