| --- |
| license: mit |
| task_categories: |
| - tabular-regression |
| tags: |
| - biology |
| pretty_name: Candida albicans Co-Expression Network |
| size_categories: |
| - 10M<n<100M |
| dataset_info: |
| - config_name: CalCEN_network |
| features: |
| - name: feature_name_1 |
| dtype: string |
| - name: feature_name_2 |
| dtype: string |
| - name: score |
| dtype: float64 |
| splits: |
| - name: train |
| num_bytes: 1472498808 |
| num_examples: 38763076 |
| download_size: 633855931 |
| dataset_size: 1472498808 |
| - config_name: blastp_network |
| features: |
| - name: feature_name_1 |
| dtype: string |
| - name: feature_name_2 |
| dtype: string |
| - name: score |
| dtype: float64 |
| splits: |
| - name: train |
| num_bytes: 4260374 |
| num_examples: 112129 |
| download_size: 1122972 |
| dataset_size: 4260374 |
| - config_name: estimated_expression |
| features: |
| - name: gene_id |
| dtype: string |
| - name: transcript_ids |
| dtype: string |
| - name: length |
| dtype: float64 |
| - name: effective_length |
| dtype: float64 |
| - name: expected_count |
| dtype: float64 |
| - name: TPM |
| dtype: float64 |
| - name: FPKM |
| dtype: float64 |
| - name: run_accession |
| dtype: string |
| - name: study_accession |
| dtype: string |
| - name: is_paired |
| dtype: bool |
| splits: |
| - name: train |
| num_bytes: 843354652 |
| num_examples: 8710174 |
| download_size: 305230791 |
| dataset_size: 843354652 |
| - config_name: sac_gene_network |
| features: |
| - name: feature_name_1 |
| dtype: string |
| - name: feature_name_2 |
| dtype: string |
| - name: score |
| dtype: float64 |
| splits: |
| - name: train |
| num_bytes: 1472498808 |
| num_examples: 38763076 |
| download_size: 452519443 |
| dataset_size: 1472498808 |
| - config_name: sac_phys_network |
| features: |
| - name: feature_name_1 |
| dtype: string |
| - name: feature_name_2 |
| dtype: string |
| - name: score |
| dtype: float64 |
| splits: |
| - name: train |
| num_bytes: 557509168 |
| num_examples: 14671296 |
| download_size: 105496144 |
| dataset_size: 557509168 |
| - config_name: top_coexp_hits |
| features: |
| - name: feature_name_1 |
| dtype: string |
| - name: feature_name_2 |
| dtype: string |
| - name: gene_name_1 |
| dtype: string |
| - name: gene_name_2 |
| dtype: string |
| - name: description_1 |
| dtype: string |
| - name: description_2 |
| dtype: string |
| - name: feature_status_1 |
| dtype: string |
| - name: feature_status_2 |
| dtype: string |
| - name: coexp_score |
| dtype: float64 |
| - name: blastp_score |
| dtype: float64 |
| - name: sac_gene_score |
| dtype: float64 |
| - name: sac_phys_score |
| dtype: float64 |
| - name: yeast_net_score |
| dtype: float64 |
| splits: |
| - name: train |
| num_bytes: 125718471 |
| num_examples: 311300 |
| download_size: 24731924 |
| dataset_size: 125718471 |
| - config_name: yeast_net_network |
| features: |
| - name: feature_name_1 |
| dtype: string |
| - name: feature_name_2 |
| dtype: string |
| - name: score |
| dtype: float64 |
| splits: |
| - name: train |
| num_bytes: 16180096 |
| num_examples: 425792 |
| download_size: 6316147 |
| dataset_size: 16180096 |
| configs: |
| - config_name: CalCEN_network |
| data_files: |
| - split: train |
| path: CalCEN_network/data/train-* |
| - config_name: blastp_network |
| data_files: |
| - split: train |
| path: blastp_network/data/train-* |
| - config_name: estimated_expression |
| data_files: |
| - split: train |
| path: estimated_expression/data/train-* |
| - config_name: sac_gene_network |
| data_files: |
| - split: train |
| path: sac_gene_network/data/train-* |
| - config_name: sac_phys_network |
| data_files: |
| - split: train |
| path: sac_phys_network/data/train-* |
| - config_name: top_coexp_hits |
| data_files: |
| - split: train |
| path: top_coexp_hits/data/train-* |
| - config_name: yeast_net_network |
| data_files: |
| - split: train |
| path: yeast_net_network/data/train-* |
| --- |
| # CalCEN: A Co-Expression Network for *Candida albicans* |
| Elucidating gene function is a major goal in biology, especially among non-model organisms. |
| However, doing so is complicated by the fact that molecular conservation does not always |
| mirror functional conservation, and that complex relationships among genes are responsible |
| for encoding pathways and higher-order biological processes. Co-expression, a promising |
| approach for predicting gene function, relies on the general principle that genes with |
| similar expression patterns across multiple conditions will likely be involved in the |
| same biological process. For *Candida albicans*, a prevalent human fungal pathogen, we |
| leveraged a large amount of publicly available transcriptomic data to generate a C. albicans |
| Co-Expression Network (CalCEN), recapitulating known protein networks, predicting gene function, and |
| enabling insights into the principles influencing co-expression. Overall, co-expression |
| is a powerful tool for uncovering gene function, and decreases the experimental tests |
| needed to identify functions for currently under-annotated genes. |
|
|
| Reference: |
|
|
| TR O'Meara, MJ O'Meara, M Sphere, 2020 |
| DeORFanizing Candida albicans Genes using Co-Expression |
| |
| Code available at: |
| http://github.com/momeara/CalCEN |
|
|
|
|
| *Candida albicans* Co-Expression Network (CalCEN) version 1.0.0 |
|
|
|
|
| ## Files ## |
| **chromsome_features.tsv** |
| - Candida albicans SC5314 chromosome features collected from Candida Genome Database 12-Jun 2018 |
| - primary key: `feature_name` |
| - URL: [http://www.candidagenome.org/download/chromosomal_feature_files/C_albicans_SC5314/C_albicans_SC5314_A22_current_chromosomal_feature.tab](http://www.candidagenome.org/download/chromosomal_feature_files/C_albicans_SC5314/C_albicans_SC5314_A22_current_chromosomal_feature.tab) |
| - tab separated table with `13,281` rows |
| ``` |
| Column: |
| feature_name <chr> "C1_00010W_A", "C1_00010W_B", "C1_00020C_A", ... |
| gene_name <chr> NA, NA, NA, NA, NA, NA, "CTA2", "CTA2", NA, ... |
| aliases <chr> "orf19.6115|C1_00010W_B|C1_00010W|orf19.1353 ... |
| feature_type <chr> "ORF|Dubious", "ORF", "ORF|Uncharacterized", ... |
| chromosome <chr> "Ca22chr1A_C_albicans_SC5314", "Ca22chr1B_C_ ... |
| start_coordinate <dbl> 4059, 4059, 4720, 4720, 8908, 8908, 10718, 1 ... |
| stop_coordinate <dbl> 4397, 4397, 4409, 4409, 8597, 8597, 11485, 1 ... |
| strand <chr> "W", "W", "C", "C", "C", "C", "W", "W", "C", ... |
| primary_cgd_id <chr> "CAL0000182519", "CAL0000183273", "CAL000018 ... |
| secondary_cgd_id <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "CAL ... |
| description <chr> "Dubious open reading frame", "Dubious open ... |
| creation_date <date> 2014-06-24, 2014-06-24, 2014-06-24, 2014-06 ... |
| sequence_coordinate_date <date> 2014-06-24, 2014-06-24, 2014-06-24, 2014-06 ... |
| gene_name_date <date> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... |
| gene_name_is_standard <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FA ... |
| sac_ortholog <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, "TUP ... |
| feature_class <chr> "ORF", "ORF", "ORF", "ORF", "ORF", "ORF", "O ... |
| feature_status <chr> "Dubious", NA, "Uncharacterized", NA, "Uncha ... |
| is_alternatively_spliced <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FA ... |
| is_transposable_element <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FA ... |
| rna_type <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, ... |
| is_blocked_reading_frame <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FA ... |
| ``` |
| |
| **genes.tsv** |
| - Curated set of `6226` genes use in this study |
| - primary key: `feature_name` |
| - foreign keys: |
| - `feature_name` -> `chromosome_features.feature_name` |
| - tab separated table with `6,226` row |
| |
| ``` |
| Column: |
| feature_name <chr> "C3_03580C_A", "C2_05660W_A", "C7_02860C_A", "C3_05180W_ ... |
| ``` |
| |
| **expression_runs.tsv** |
| - Curated set of RNA-seq runs used in this study |
| - Collected from NCBI SRA |
| - primary key: `run_accession` |
| - tab separated table with `853` rows |
| ``` |
| Column: |
| submission_accession <chr> "ERA237292", "ERA237292", "ERA237292", ... |
| submission_lab <chr> "ArrayExpress", "ArrayExpress", "ArrayE ... |
| updated_date <date> 2016-01-11, 2016-01-11, 2016-01-11, 20 ... |
| sradb_updated <dttm> 2018-05-24 18:09:52, 2018-05-24 18:09: ... |
| study_accession <chr> "ERP003535", "ERP003535", "ERP003535", ... |
| study_alias <chr> "E-MTAB-1720", "E-MTAB-1720", "E-MTAB-1 ... |
| study_name <chr> "E-MTAB-1720", "E-MTAB-1720", "E-MTAB-1 ... |
| study_title <chr> "Initial stress responses of Candida al ... |
| study_type <chr> "Transcriptome Analysis", "Transcriptom ... |
| study_abstract <chr> "A study was carried out to characteris ... |
| center_project_name <chr> "Initial stress responses of Candida al ... |
| study_description <chr> "A study was carried out to characteris ... |
| study_attribute <chr> "ArrayExpress: E-MTAB-1720", "ArrayExpr ... |
| description <chr> "Protocols: Candida albicans (strain CA ... |
| design_description <chr> "Initial stress responses of Candida al ... |
| sample_accession <chr> "ERS323180", "ERS323177", "ERS323173", ... |
| sample_alias <chr> "E-MTAB-1720:NS B", "E-MTAB-1720:XS+NS ... |
| sample_name <chr> "E-MTAB-1720:NS B", "E-MTAB-1720:XS+NS ... |
| sample_attribute <chr> "organism: Candida albicans || genotype ... |
| taxon_id <dbl> 5476, 5476, 5476, 5476, 5476, 5476, 547 ... |
| background_strain <chr> "CAI4", "CAI4", "CAI4", "CAI4", "CAI4", ... |
| platform <chr> "ILLUMINA", "ILLUMINA", "ILLUMINA", "IL ... |
| platform_parameters <chr> "INSTRUMENT_MODEL: Illumina HiSeq 2000" ... |
| instrument_model <chr> "Illumina HiSeq 2000", "Illumina HiSeq ... |
| library_name <chr> "NS B", "XS+NS D", "NS D", "XS+NS D", " ... |
| library_strategy <chr> "RNA-Seq", "RNA-Seq", "RNA-Seq", "RNA-S ... |
| library_source <chr> "TRANSCRIPTOMIC", "TRANSCRIPTOMIC", "TR ... |
| library_selection <chr> "cDNA", "cDNA", "cDNA", "cDNA", "cDNA", ... |
| library_layout <chr> "SINGLE -", "SINGLE -", "SINGLE -", "SI ... |
| library_construction_protocol <chr> "Candida albicans (strain CAI4-CIp10) w ... |
| is_paired <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALS ... |
| read_spec <chr> "READ_INDEX: 0; READ_CLASS: Application ... |
| experiment_accession <chr> "ERX283431", "ERX283301", "ERX283317", ... |
| experiment_alias <chr> "E-MTAB-1720:120314_0166_D0814ACXX_3_SA ... |
| experiment_name <chr> "E-MTAB-1720:120314_0166_D0814ACXX_3_SA ... |
| experiment_title <chr> "Illumina HiSeq 2000 sequencing; Initia ... |
| experiment_attribute <chr> "Experimental Factor: compound_1: DPTA ... |
| run_accession <chr> "ERR310125", "ERR310018", "ERR309994", ... |
| run_alias <chr> "E-MTAB-1720:120314_0166_D0814ACXX_3_SA ... |
| run_center <chr> "The GenePool, University of Edinburgh" ... |
| spots <dbl> 1879764, 6330342, 5750605, 7088156, 649 ... |
| bases <dbl> 95867964, 322847442, 293280855, 3614959 ... |
| sra_fname <chr> "/nfs/ex7/work/momeara/ca_coexp/sra_806 ... |
| year_collected <dbl> 2018, 2018, 2018, 2018, 2018, 2018, 201 ... |
| ``` |
|
|
| **estimated_expression.tsv** |
| - gene by RNA-seq run expression levels |
| - primary key: `gene_id`, `run_accession` |
| - foreign keys: |
| - `gene_id` -> `genes.feature_name` |
| - `run_accession` -> `expression_runs.run_accession` |
| - The FPKM column represents the per-gene, per-run expression level |
| - tab separated table with `8,710,174` rows |
| ``` |
| Column: |
| gene_id <chr> "C1_00010W_A", "C1_00020C_A", "C1_00030C_A", "C1_000 ... |
| transcript_ids <chr> "C1_00010W_A", "C1_00020C_A", "C1_00030C_A", "C1_000 ... |
| length <dbl> 339, 312, 312, 768, 348, 1539, 1089, 852, 522, 729, ... |
| effective_length <dbl> 290, 263, 263, 719, 299, 1490, 1040, 803, 473, 680, ... |
| expected_count <dbl> 24.00, 2149.00, 355.01, 3219.94, 56.00, 8003.00, 696 ... |
| TPM <dbl> 3.38, 333.77, 55.14, 182.93, 7.65, 219.40, 273.72, 4 ... |
| FPKM <dbl> 4.36, 430.27, 71.08, 235.82, 9.86, 282.83, 352.86, 5 ... |
| run_accession <chr> "ERR1143627", "ERR1143627", "ERR1143627", "ERR114362 ... |
| study_accession <chr> "ERP013259", "ERP013259", "ERP013259", "ERP013259", ... |
| is_paired <lgl> FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FAL ... |
| ``` |
| |
| **CalCEN_network.tsv** |
| - Co-expression network |
| - primary key: `feature_name_1`, `feature_name_2` |
| - foreign keys: |
| - `feature_name_1` -> `genes.feature_name` |
| - `feature_name_2` -> `genes.feature_name` |
| - score represents the scaled rank of the association between genes among |
| all gene pairs. |
| - `score >= .99` is the default threshold for a significant association |
| - tab separated table with `38,763,076` rows |
| ``` |
| Column: |
| feature_name_1 <chr> "C3_03580C_A", "C2_05660W_A", "C7_02860C_A", "C3_05180 ... |
| feature_name_2 <chr> "C3_03580C_A", "C3_03580C_A", "C3_03580C_A", "C3_03580 ... |
| score <dbl> 1.00000000, 0.75060056, 0.40875062, 0.68047576, 0.3594 ... |
| ``` |
| |
| **blastp_network.tsv** |
| - blastp sequence similarity network |
| - primary key: `feature_name_1`, `feature_name_2` |
| - foreign keys: |
| - `feature_name_1` -> `genes.feature_name` |
| - `feature_name_2` -> `genes.feature_name` |
| - score representes the scaled rank of the blastp Z-score among |
| all significant gene pair associations (i.e. missing -> `score = 0`). |
| - tab separated table with `112,129` rows |
| ``` |
| Column: |
| feature_name_1 <chr> "C3_03580C_A", "C1_08890C_A", "CR_06460W_A", "C3_03600 ... |
| feature_name_2 <chr> "C3_03580C_A", "C3_03580C_A", "C3_03580C_A", "C3_03580 ... |
| score <dbl> 0.95015957, 0.18948743, 0.27596712, 0.89713733, 0.0849 ... |
| ``` |
| |
| **sac_gene.tsv** |
| - genetic associations between orthologous Sac genes Network |
| - primary key: `feature_name_1`, `feature_name_2` |
| - foreign keys: |
| - `feature_name_1` -> `genes.feature_name` |
| - `feature_name_2` -> `genes.feature_name` |
| - score represents the scaled rank of the the spearman correlation between |
| between binary genetic association collected from BioGRID between orthologous genes |
| from sac (higher is more siginficant) |
| - tab separated table with `38,763,076` rows |
| ``` |
| Column: |
| feature_name_1 <chr> "C3_03580C_A", "C2_05660W_A", "C7_02860C_A", "C3_05180 ... |
| feature_name_2 <chr> "C3_03580C_A", "C3_03580C_A", "C3_03580C_A", "C3_03580 ... |
| score <dbl> 1.00000000, 0.61167254, 0.23926432, 0.40917646, 0.6116 ... |
| ``` |
| |
| **sac_gene.tsv** |
| - physical protein-protein interaction between orthologous Sac genes Network |
| - primary key: `feature_name_1`, `feature_name_2` |
| - foreign keys: |
| - `feature_name_1` -> `genes.feature_name` |
| - `feature_name_2` -> `genes.feature_name` |
| - score represents the scaled rank of the the extended binary network |
| between binary genetic association collected from BioGRID between orthologous genes |
| from sac (higher is more siginficant). |
| - tab separated table with `14,671,296` rows and columns |
| ``` |
| Column: |
| feature_name_1 <chr> "C3_03580C_A", "C2_05660W_A", "C7_02860C_A", "C3_05180 ... |
| feature_name_2 <chr> "C3_03580C_A", "C2_05660W_A", "C7_02860C_A", "C7_02860 ... |
| score <dbl> 1.0000000, 1.0000000, 1.0000000, 0.5000000, 0.5000000, ... |
| ``` |
| |
| **yeast_net_network.tsv** |
| - YeastNet between orthologous Sac genes network |
| - primary key: `feature_name_1`, `feature_name_2` |
| - foreign keys: |
| - `feature_name_1` -> `genes.feature_name` |
| - `feature_name_2` -> `genes.feature_name` |
| - score is taken directly from the YeastNet network |
| - tab separated table with `425,792` rows |
| ``` |
| Column: |
| feature_name_1 <chr> "C1_12750C_A", "C5_05140W_A", "CR_07620W_A", "C7_04040 ... |
| feature_name_2 <chr> "C7_02860C_A", "C7_02860C_A", "C7_02860C_A", "C7_02860 ... |
| score <dbl> 2.300967, 2.415099, 2.300967, 2.309640, 2.337247, 2.22 ... |
| ``` |
| |
| **go_annotations.tsv** |
| - GO annotations from Candida Genome Database collected 12-Jun 2018 |
| - URL: [http://www.candidagenome.org/download/go/gene_association.cgd.gz](http://www.candidagenome.org/download/go/gene_association.cgd.gz) |
| - primary key: `feature_name`, `go_id` |
| - foreign keys: |
| - `feature_name` -> `genes.feature_name` |
| - values exclude NOT annotations and are propagated up the ontological hierarchy |
| - tab separated table with `29,159` rows |
| ``` |
| Column: |
| feature_name <chr> "C1_00100C_A", "C1_00640C_A", "C1_02660C_A", "C1_03540C_ ... |
| go_id <chr> "GO.0000002", "GO.0000002", "GO.0000002", "GO.0000002", ... |
| ``` |
|
|
| **gba_summary.tsv** |
| - Summary of guilt-by-association gene-function prediction |
| - primary key: `anno_id`, `network_id` |
| - `anno_id` in [all, MF, BB, CC] |
| - `network_id` is a set of networks ids separated by '|' |
| - `auroc_mean` is the mean area under the ROC curve summarized over 10-fold cross validation and `auroc_std` is the standard deviation |
| - `degree_null_auroc_mean` is the degree null predictor scores and `degree_null_auroc_std` is the standard deviation |
| - tab separated table with `125` rows |
| ``` |
| Column: |
| anno_id <chr> "all", "all", "all", "all", "all", "all", "all ... |
| network_id <chr> "CalCEN", "BlastP", "SacPhys", "SacGene", "Yea ... |
| auroc_mean <dbl> 0.7522911, 0.6880802, 0.7713754, 0.7525273, 0. ... |
| auroc_std <dbl> 0.08311475, 0.11720483, 0.17135738, 0.12416886 ... |
| degree_null_auroc_mean <dbl> 0.5111914, 0.5473948, 0.5996210, 0.5926223, 0. ... |
| degree_null_auroc_std <dbl> 0.1069059, 0.1418470, 0.1340942, 0.1316009, 0. ... |
| ``` |
