Hugging Face's logo

Datasets:
wei82
/
precancer-omics-data

Languages:
English
Size:
n>1T
Tags:
biology
medical
cancer
oncology
single-cell
scRNA-seq
License:
Dataset card Files
xet
 Community
wei82 commited on
Commit
45df8f3
·
verified ·
1 Parent(s): 6d3c17d

fill cBioPortal:brca_cptac_2020 (38 files, 158.9 MB) [audit-fill]

Browse files
Files changed (39) hide show
  1. .gitattributes +6 -0
  2. data/cBioPortal/brca_cptac_2020/LICENSE +1 -0
  3. data/cBioPortal/brca_cptac_2020/README.md +42 -0
  4. data/cBioPortal/brca_cptac_2020/case_lists/cases_3way_complete.txt +6 -0
  5. data/cBioPortal/brca_cptac_2020/case_lists/cases_acetylprotein_quantification.txt +5 -0
  6. data/cBioPortal/brca_cptac_2020/case_lists/cases_all.txt +6 -0
  7. data/cBioPortal/brca_cptac_2020/case_lists/cases_cna.txt +6 -0
  8. data/cBioPortal/brca_cptac_2020/case_lists/cases_cnaseq.txt +6 -0
  9. data/cBioPortal/brca_cptac_2020/case_lists/cases_expression.txt +6 -0
  10. data/cBioPortal/brca_cptac_2020/case_lists/cases_log2CNA.txt +6 -0
  11. data/cBioPortal/brca_cptac_2020/case_lists/cases_mRNA_U133.txt +6 -0
  12. data/cBioPortal/brca_cptac_2020/case_lists/cases_phosphoprotein_quantification.txt +5 -0
  13. data/cBioPortal/brca_cptac_2020/case_lists/cases_protein_quantification.txt +6 -0
  14. data/cBioPortal/brca_cptac_2020/case_lists/cases_sequenced.txt +6 -0
  15. data/cBioPortal/brca_cptac_2020/data_acetylprotein_quantification.txt +0 -0
  16. data/cBioPortal/brca_cptac_2020/data_clinical_patient.txt +127 -0
  17. data/cBioPortal/brca_cptac_2020/data_clinical_sample.txt +127 -0
  18. data/cBioPortal/brca_cptac_2020/data_cna.txt +0 -0
  19. data/cBioPortal/brca_cptac_2020/data_gene_panel_matrix.txt +123 -0
  20. data/cBioPortal/brca_cptac_2020/data_log2_cna.txt +3 -0
  21. data/cBioPortal/brca_cptac_2020/data_mrna_seq_fpkm.txt +3 -0
  22. data/cBioPortal/brca_cptac_2020/data_mrna_seq_fpkm_zscores_ref_all_samples.txt +3 -0
  23. data/cBioPortal/brca_cptac_2020/data_mutations.txt +3 -0
  24. data/cBioPortal/brca_cptac_2020/data_phosphoprotein_quantification.txt +3 -0
  25. data/cBioPortal/brca_cptac_2020/data_protein_quantification.txt +0 -0
  26. data/cBioPortal/brca_cptac_2020/data_protein_quantification_zscores_ref_all_samples.txt +3 -0
  27. data/cBioPortal/brca_cptac_2020/meta_acetylprotein_quantification.txt +10 -0
  28. data/cBioPortal/brca_cptac_2020/meta_clinical_patient.txt +4 -0
  29. data/cBioPortal/brca_cptac_2020/meta_clinical_sample.txt +4 -0
  30. data/cBioPortal/brca_cptac_2020/meta_cna.txt +8 -0
  31. data/cBioPortal/brca_cptac_2020/meta_gene_panel_matrix.txt +4 -0
  32. data/cBioPortal/brca_cptac_2020/meta_log2_cna.txt +8 -0
  33. data/cBioPortal/brca_cptac_2020/meta_mrna_seq_fpkm.txt +8 -0
  34. data/cBioPortal/brca_cptac_2020/meta_mrna_seq_fpkm_zscores_ref_all_samples.txt +8 -0
  35. data/cBioPortal/brca_cptac_2020/meta_mutations.txt +8 -0
  36. data/cBioPortal/brca_cptac_2020/meta_phosphoprotein_quantification.txt +10 -0
  37. data/cBioPortal/brca_cptac_2020/meta_protein_quantification.txt +8 -0
  38. data/cBioPortal/brca_cptac_2020/meta_protein_quantification_zscores_ref_all_samples.txt +8 -0
  39. data/cBioPortal/brca_cptac_2020/meta_study.txt +9 -0
.gitattributes CHANGED
@@ -974,3 +974,9 @@ data/cBioPortal/brca_tcga_pub2015/data_mrna_seq_v2_rsem_zscores_ref_diploid_samp
974
  data/cBioPortal/brca_tcga_pub2015/data_mutations.txt filter=lfs diff=lfs merge=lfs -text
975
  data/cBioPortal/crc_hta8_htan_2024/data_pseudo_bulk_rna_seq_cpm_zscores_ref_all_samples.txt filter=lfs diff=lfs merge=lfs -text
976
  data/cBioPortal/cscc_ranson_2022/data_mutations.txt filter=lfs diff=lfs merge=lfs -text
 
 
 
 
 
 
 
974
  data/cBioPortal/brca_tcga_pub2015/data_mutations.txt filter=lfs diff=lfs merge=lfs -text
975
  data/cBioPortal/crc_hta8_htan_2024/data_pseudo_bulk_rna_seq_cpm_zscores_ref_all_samples.txt filter=lfs diff=lfs merge=lfs -text
976
  data/cBioPortal/cscc_ranson_2022/data_mutations.txt filter=lfs diff=lfs merge=lfs -text
977
+ data/cBioPortal/brca_cptac_2020/data_log2_cna.txt filter=lfs diff=lfs merge=lfs -text
978
+ data/cBioPortal/brca_cptac_2020/data_mrna_seq_fpkm.txt filter=lfs diff=lfs merge=lfs -text
979
+ data/cBioPortal/brca_cptac_2020/data_mrna_seq_fpkm_zscores_ref_all_samples.txt filter=lfs diff=lfs merge=lfs -text
980
+ data/cBioPortal/brca_cptac_2020/data_mutations.txt filter=lfs diff=lfs merge=lfs -text
981
+ data/cBioPortal/brca_cptac_2020/data_phosphoprotein_quantification.txt filter=lfs diff=lfs merge=lfs -text
982
+ data/cBioPortal/brca_cptac_2020/data_protein_quantification_zscores_ref_all_samples.txt filter=lfs diff=lfs merge=lfs -text
data/cBioPortal/brca_cptac_2020/LICENSE ADDED
@@ -0,0 +1 @@
 
 
1
+ The data are available under the ODC Open Database License (ODbL)(http://opendatacommons.org/licenses/odbl/1.0/) (summary available here: http://www.opendatacommons.org/licenses/odbl/1-0/summary/): you are free to share and modify the data so long as you attribute any public use of the database, or works produced from the database; keep the resulting data-sets open; and offer your shared or adapted version of the data-set under the same ODbL license.
data/cBioPortal/brca_cptac_2020/README.md ADDED
@@ -0,0 +1,42 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # Data transformation of brca_broad_2020
2
+
3
+ Article: Krug et al. 2020 Cell. https://www.cell.com/cell/fulltext/S0092-8674(20)31400-8
4
+
5
+ Data was downloaded from the supplementary files:
6
+ - Table S1: Metadata and mutation data
7
+ - Table S2: Proteome data, phosphoproteome data, acetylproteome data, mRNA expression data, CNA data
8
+
9
+
10
+ ## Notes on data transformation
11
+
12
+ Metadata
13
+ - Clinical data was directly inferred from the Excel sheet. Manual distinction as made on patient/sample attributes.
14
+ - Data contained 1 sample per patient
15
+
16
+ Mutation data
17
+
18
+ - The MAF was filtered according to the following algorithm (based on https://doi.org/10.1016/j.ccell.2020.10.015):
19
+ remove mutation if VAF (t_alt_count / (t_ref_count + t_alt_count)) <= 0.65 and AF in any population annotation (1000 genomes, etc.) > .001
20
+ In addition, it was checked against germline calls, removing one additional call that was likely missed because the hg19 annotation data source used is somewhat out of date. In total 655 mutations out of 29,673 were filtered out that way.
21
+
22
+ Protein data
23
+ - Gene symbols were inferred from Ensembl Biomart from the Refseq Protein IDs
24
+ - For duplicate genes, rows were collapsed and the average values were used
25
+ - Z-scores were calculated from all tumor samples in the study
26
+
27
+ Phosphoproteome and acetylproteome data
28
+ - Transformed to GENERIC_ASSAY since only a single protein quantification profile is allowed
29
+ - gene symbols were inferred from Ensembl Biomart from the Refseq Protein IDs
30
+ - ENTITY_STABLE_ID constructed in the form <gene_symbol>_<mod_sites>
31
+ - in case of duplicate entries, a suffix of "__n_" was added to the ID.
32
+ - Column is added (PHOSPHOSITES/ACETYLSITES) to indicate detailed modification sites information
33
+ - From the documention in supplementary table S2:
34
+ >Unique identifier for each phosphosite (VM, variable modification) with RefseqProteinID_sites_#sitesPresent_#sitesLocalized_firstSite_lastSite. The numbers in sites, firstSite, lastSite indicate the amino acid position in the protein sequence of accession_number. The N-terminal amino acid of the protein is position 1. The purpose of firstSite and lastSite is to provide a range of possibilities when unlocalized sites are present (#sitesLocalized < #sitesPresent).
35
+
36
+ Expression data
37
+ - FPKM values directly inferred from the table (values of 0 were considered as missing values and replaced by NA before applying log2 transformation)
38
+ - Z-scores calculated from all tumor samples
39
+
40
+ CNA data
41
+ - Continuous data was inferred from the table
42
+ - Discrete CNA calls were delivered by the authors upon request
data/cBioPortal/brca_cptac_2020/case_lists/cases_3way_complete.txt ADDED
@@ -0,0 +1,6 @@
 
 
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ stable_id: brca_cptac_2020_3way_complete
3
+ case_list_name: Samples with mutation, CNA, and expression data
4
+ case_list_description: Samples with available mutation data, copy number alteration and gene expression data
5
+ case_list_category: all_cases_with_mutation_and_cna_and_mrna_data
6
+ case_list_ids: X05BR026 X11BR047 X11BR009 X11BR072 X05BR001 X11BR059 X11BR053 X13BR009 X20BR002 X05BR009 X11BR011 X11BR051 X01BR030 X20BR001 X11BR040 X09BR001 X11BR020 X01BR025 X01BR008 X01BR040 CPT001846 X14BR005 X21BR010 X01BR009 X14BR008 X11BR044 X03BR011 X20BR007 X20BR006 X05BR003 X11BR042 X01BR010 X01BR031 X01BR026 X11BR036 X05BR045 X11BR004 X01BR017 X11BR043 X09BR004 X11BR050 X11BR074 X18BR006 X01BR027 X06BR014 X22BR006 X11BR031 X11BR030 X11BR032 X18BR017 X11BR058 X01BR018 X20BR008 X05BR044 X05BR038 X14BR014 X01BR032 X01BR033 X05BR042 X06BR003 X09BR005 X03BR006 X05BR004 X11BR018 X03BR010 X11BR015 X11BR049 X11BR019 X11BR025 X11BR056 X11BR080 X01BR015 X01BR001 X01BR023 X16BR012 X18BR019 X11BR010 X15BR003 X11BR017 X18BR009 X18BR010 X11BR073 X03BR013 X11BR060 X03BR002 X18BR002 X05BR029 X06BR006 X05BR005 X09BR007 X11BR013 X22BR005 CPT000814 X11BR038 X11BR028 X11BR006 X11BR012 X11BR003 X20BR005 X11BR022 X18BR007 X01BR042 X18BR016 X11BR027 X11BR075 X18BR004 X03BR004 X05BR016 X21BR002 X11BR055 X03BR005 X11BR016 X21BR001 X01BR020 X01BR043 X11BR023 X18BR003 X11BR014 X11BR054 X11BR024 X05BR043 X06BR005
data/cBioPortal/brca_cptac_2020/case_lists/cases_acetylprotein_quantification.txt ADDED
@@ -0,0 +1,5 @@
 
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ stable_id: brca_cptac_2020_acetylprotein_quantification
3
+ case_list_name: Samples with acetylprotein quantification data
4
+ case_list_description: Samples with acetylprotein quantification data by mass spectrometry
5
+ case_list_ids: CPT000814 CPT001846 X01BR001 X01BR008 X01BR009 X01BR010 X01BR015 X01BR017 X01BR018 X01BR020 X01BR023 X01BR025 X01BR026 X01BR027 X01BR030 X01BR031 X01BR032 X01BR033 X01BR040 X01BR042 X01BR043 X03BR002 X03BR004 X03BR005 X03BR006 X03BR010 X03BR011 X03BR013 X05BR001 X05BR003 X05BR004 X05BR005 X05BR009 X05BR016 X05BR026 X05BR029 X05BR038 X05BR042 X05BR043 X05BR044 X05BR045 X06BR003 X06BR005 X06BR006 X06BR014 X09BR001 X09BR004 X09BR005 X09BR007 X11BR003 X11BR004 X11BR006 X11BR009 X11BR010 X11BR011 X11BR012 X11BR013 X11BR014 X11BR015 X11BR016 X11BR017 X11BR018 X11BR019 X11BR020 X11BR022 X11BR023 X11BR024 X11BR025 X11BR027 X11BR028 X11BR030 X11BR031 X11BR032 X11BR036 X11BR038 X11BR040 X11BR042 X11BR043 X11BR044 X11BR047 X11BR049 X11BR050 X11BR051 X11BR053 X11BR054 X11BR055 X11BR056 X11BR058 X11BR059 X11BR060 X11BR072 X11BR073 X11BR074 X11BR075 X11BR080 X13BR009 X14BR005 X14BR008 X14BR014 X15BR003 X16BR012 X18BR002 X18BR003 X18BR004 X18BR006 X18BR007 X18BR009 X18BR010 X18BR016 X18BR017 X18BR019 X20BR001 X20BR002 X20BR005 X20BR006 X20BR007 X20BR008 X21BR001 X21BR002 X21BR010 X22BR005 X22BR006
data/cBioPortal/brca_cptac_2020/case_lists/cases_all.txt ADDED
@@ -0,0 +1,6 @@
 
 
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ stable_id: brca_cptac_2020_all
3
+ case_list_name: All samples
4
+ case_list_description: All samples (122 samples)
5
+ case_list_category: all_cases_in_study
6
+ case_list_ids: X14BR008 X16BR012 X14BR005 X01BR033 X09BR001 CPT001846 X09BR007 X03BR013 X03BR010 X03BR011 X01BR020 X01BR023 X01BR025 X15BR003 X01BR027 X01BR026 X01BR030 X22BR005 X22BR006 X11BR024 X11BR025 X05BR038 X11BR027 X11BR020 X11BR022 X11BR023 X11BR060 X11BR028 X21BR010 X06BR006 X05BR016 X18BR016 CPT000814 X03BR002 X03BR005 X03BR004 X18BR010 X03BR006 X11BR019 X05BR044 X18BR019 X01BR018 X06BR005 X06BR003 X01BR010 X01BR015 X01BR017 X11BR036 X05BR029 X11BR032 X11BR031 X11BR030 X11BR073 X11BR072 X05BR026 X11BR075 X11BR074 X18BR009 X05BR005 X05BR004 X05BR003 X09BR005 X09BR004 X05BR043 X05BR042 X18BR003 X18BR002 X18BR004 X05BR009 X18BR006 X11BR080 X13BR009 X05BR045 X11BR012 X06BR014 X11BR013 X01BR009 X11BR009 X01BR043 X01BR042 X18BR017 X01BR040 X11BR003 X01BR001 X11BR006 X11BR004 X11BR014 X11BR049 X11BR047 X11BR044 X11BR042 X11BR043 X11BR040 X21BR001 X14BR014 X21BR002 X01BR008 X18BR007 X20BR006 X20BR007 X20BR005 X20BR002 X11BR018 X20BR001 X11BR015 X20BR008 X11BR017 X11BR016 X11BR011 X11BR010 X05BR001 X01BR031 X11BR051 X11BR050 X11BR053 X01BR032 X11BR055 X11BR054 X11BR056 X11BR059 X11BR058 X11BR038
data/cBioPortal/brca_cptac_2020/case_lists/cases_cna.txt ADDED
@@ -0,0 +1,6 @@
 
 
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ stable_id: brca_cptac_2020_cna
3
+ case_list_name: Samples with CNA data
4
+ case_list_description: Samples with CNA data (122 samples)
5
+ case_list_category: all_cases_with_cna_data
6
+ case_list_ids: X14BR008 X16BR012 X14BR005 X01BR033 X09BR001 CPT001846 X09BR007 X03BR013 X03BR010 X03BR011 X01BR020 X01BR023 X01BR025 X15BR003 X01BR027 X01BR026 X01BR030 X22BR005 X22BR006 X11BR024 X11BR025 X05BR038 X11BR027 X11BR020 X11BR022 X11BR023 X11BR060 X11BR028 X21BR010 X06BR006 X05BR016 X18BR016 CPT000814 X03BR002 X03BR005 X03BR004 X18BR010 X03BR006 X11BR019 X05BR044 X18BR019 X01BR018 X06BR005 X06BR003 X01BR010 X01BR015 X09BR005 X01BR017 X11BR036 X05BR029 X11BR032 X11BR031 X11BR030 X11BR073 X11BR072 X05BR026 X11BR075 X11BR074 X18BR009 X05BR005 X05BR004 X05BR003 X05BR001 X09BR004 X05BR043 X05BR042 X18BR003 X18BR002 X18BR004 X05BR009 X18BR006 X11BR080 X13BR009 X05BR045 X11BR012 X06BR014 X11BR013 X01BR009 X11BR009 X01BR043 X01BR042 X18BR017 X01BR040 X11BR003 X01BR001 X11BR006 X11BR004 X11BR049 X11BR047 X11BR044 X11BR042 X11BR043 X11BR040 X21BR001 X14BR014 X21BR002 X01BR008 X18BR007 X20BR006 X20BR007 X20BR005 X20BR002 X11BR018 X20BR001 X11BR015 X11BR014 X11BR017 X11BR016 X11BR011 X11BR010 X20BR008 X01BR031 X11BR051 X11BR050 X11BR053 X01BR032 X11BR055 X11BR054 X11BR056 X11BR059 X11BR058 X11BR038
data/cBioPortal/brca_cptac_2020/case_lists/cases_cnaseq.txt ADDED
@@ -0,0 +1,6 @@
 
 
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ stable_id: brca_cptac_2020_cnaseq
3
+ case_list_name: Samples with mutation and CNA data
4
+ case_list_description: Samples with mutation and CNA data (122 samples)
5
+ case_list_category: all_cases_with_mutation_and_cna_data
6
+ case_list_ids: X14BR008 X14BR005 X01BR020 X01BR023 X01BR025 X15BR003 X01BR027 X01BR026 X22BR005 X22BR006 X11BR060 X01BR018 X05BR016 X18BR016 X18BR017 X18BR010 X18BR019 X11BR073 X11BR072 X11BR075 X11BR074 X18BR009 X09BR001 X05BR004 X05BR003 X09BR005 X09BR004 X18BR003 X18BR002 X18BR004 X18BR007 X18BR006 X01BR043 X01BR042 X01BR040 X11BR049 X11BR047 X11BR044 X11BR042 X11BR043 X11BR040 X20BR006 X20BR007 X20BR005 X20BR002 X20BR001 X20BR008 X11BR051 X11BR050 X11BR053 X11BR055 X11BR054 X11BR056 X11BR059 X11BR058 X16BR012 X05BR005 CPT001846 X09BR007 X03BR013 X03BR010 X03BR011 X05BR001 X11BR024 X11BR025 X05BR038 X11BR027 X11BR020 X11BR022 X11BR023 X11BR028 X03BR002 X03BR005 X05BR009 X03BR006 X06BR006 X06BR005 X06BR003 X01BR010 X01BR015 X01BR017 X11BR036 X05BR029 X11BR032 X11BR031 X11BR030 X05BR026 X11BR038 X05BR043 X05BR042 X21BR010 X05BR045 X05BR044 X11BR080 X13BR009 X11BR012 X06BR014 X01BR009 X01BR008 X11BR003 X01BR001 X11BR006 X11BR004 X11BR011 X21BR001 X14BR014 X21BR002 X11BR009 X11BR010 X11BR019 X11BR018 CPT000814 X11BR015 X11BR014 X11BR017 X11BR016 X01BR032 X01BR033 X01BR030 X01BR031 X11BR013 X03BR004
data/cBioPortal/brca_cptac_2020/case_lists/cases_expression.txt ADDED
@@ -0,0 +1,6 @@
 
 
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ stable_id: brca_cptac_2020_rna_seq_mrna
3
+ case_list_name: Samples with gene expression data
4
+ case_list_description: Samples with gene expression data by RNA-Seq
5
+ case_list_category: all_cases_with_mrna_rnaseq_data
6
+ case_list_ids: CPT000814 CPT001846 X01BR001 X01BR008 X01BR009 X01BR010 X01BR015 X01BR017 X01BR018 X01BR020 X01BR023 X01BR025 X01BR026 X01BR027 X01BR030 X01BR031 X01BR032 X01BR033 X01BR040 X01BR042 X01BR043 X03BR002 X03BR004 X03BR005 X03BR006 X03BR010 X03BR011 X03BR013 X05BR001 X05BR003 X05BR004 X05BR005 X05BR009 X05BR016 X05BR026 X05BR029 X05BR038 X05BR042 X05BR043 X05BR044 X05BR045 X06BR003 X06BR005 X06BR006 X06BR014 X09BR001 X09BR004 X09BR005 X09BR007 X11BR003 X11BR004 X11BR006 X11BR009 X11BR010 X11BR011 X11BR012 X11BR013 X11BR014 X11BR015 X11BR016 X11BR017 X11BR018 X11BR019 X11BR020 X11BR022 X11BR023 X11BR024 X11BR025 X11BR027 X11BR028 X11BR030 X11BR031 X11BR032 X11BR036 X11BR038 X11BR040 X11BR042 X11BR043 X11BR044 X11BR047 X11BR049 X11BR050 X11BR051 X11BR053 X11BR054 X11BR055 X11BR056 X11BR058 X11BR059 X11BR060 X11BR072 X11BR073 X11BR074 X11BR075 X11BR080 X13BR009 X14BR005 X14BR008 X14BR014 X15BR003 X16BR012 X18BR002 X18BR003 X18BR004 X18BR006 X18BR007 X18BR009 X18BR010 X18BR016 X18BR017 X18BR019 X20BR001 X20BR002 X20BR005 X20BR006 X20BR007 X20BR008 X21BR001 X21BR002 X21BR010 X22BR005 X22BR006
data/cBioPortal/brca_cptac_2020/case_lists/cases_log2CNA.txt ADDED
@@ -0,0 +1,6 @@
 
 
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ stable_id: brca_cptac_2020_log2CNA
3
+ case_list_name: Samples with log2 copy-number data
4
+ case_list_description: Samples with log2 copy-number data (122 samples)
5
+ case_list_category: all_cases_with_log2_cna_data
6
+ case_list_ids: X14BR008 X14BR005 X01BR020 X01BR023 X01BR025 X15BR003 X01BR027 X01BR026 X22BR005 X22BR006 X11BR060 X01BR018 X05BR016 X18BR016 CPT000814 X18BR010 X18BR019 X11BR073 X11BR072 X11BR075 X11BR074 X18BR009 X05BR005 X05BR004 X05BR003 X05BR001 X09BR004 X18BR003 X18BR002 X18BR004 X05BR009 X18BR006 X01BR043 X01BR042 X01BR040 X11BR049 X11BR047 X11BR044 X11BR042 X11BR043 X11BR040 X20BR006 X20BR007 X20BR005 X20BR002 X20BR001 X20BR008 X11BR051 X11BR050 X11BR053 X11BR055 X11BR054 X11BR056 X11BR059 X11BR058 X16BR012 X09BR001 CPT001846 X09BR007 X03BR013 X03BR010 X03BR011 X09BR005 X11BR024 X11BR025 X05BR038 X11BR027 X11BR020 X11BR022 X11BR023 X11BR028 X03BR002 X03BR005 X03BR004 X03BR006 X06BR006 X06BR005 X06BR003 X01BR010 X01BR015 X01BR017 X11BR036 X05BR029 X11BR032 X11BR031 X11BR030 X05BR026 X11BR038 X05BR043 X05BR042 X21BR010 X05BR045 X05BR044 X11BR080 X13BR009 X01BR031 X06BR014 X01BR009 X11BR009 X11BR003 X01BR001 X11BR006 X11BR004 X11BR011 X21BR001 X14BR014 X21BR002 X01BR008 X11BR010 X18BR007 X11BR019 X11BR018 X18BR017 X11BR015 X11BR014 X11BR017 X11BR016 X01BR032 X01BR033 X01BR030 X11BR012 X11BR013
data/cBioPortal/brca_cptac_2020/case_lists/cases_mRNA_U133.txt ADDED
@@ -0,0 +1,6 @@
 
 
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ stable_id: brca_cptac_2020_mrna_U133
3
+ case_list_name: Samples with mRNA data (U133 microarray only)
4
+ case_list_description: Samples with mRNA expression data (122 samples)
5
+ case_list_category: all_cases_with_mrna_array_data
6
+ case_list_ids: X14BR008 X14BR005 X01BR020 X01BR023 X01BR025 X15BR003 X01BR027 X01BR026 X22BR005 X22BR006 X11BR060 X01BR018 X05BR016 X18BR016 CPT000814 X18BR010 X18BR019 X11BR073 X11BR072 X11BR075 X11BR074 X18BR009 X05BR005 X05BR004 X05BR003 X05BR001 X09BR004 X18BR003 X18BR002 X18BR004 X05BR009 X18BR006 X01BR043 X01BR042 X01BR040 X11BR049 X11BR047 X11BR044 X11BR042 X11BR043 X11BR040 X20BR006 X20BR007 X20BR005 X20BR002 X20BR001 X20BR008 X11BR051 X11BR050 X11BR053 X11BR055 X11BR054 X11BR056 X11BR059 X11BR058 X16BR012 X09BR001 CPT001846 X09BR007 X03BR013 X03BR010 X03BR011 X09BR005 X11BR024 X11BR025 X05BR038 X11BR027 X11BR020 X11BR022 X11BR023 X11BR028 X03BR002 X03BR005 X03BR004 X03BR006 X06BR006 X06BR005 X06BR003 X01BR010 X01BR015 X01BR017 X11BR036 X05BR029 X11BR032 X11BR031 X11BR030 X05BR026 X11BR038 X05BR043 X05BR042 X21BR010 X05BR045 X05BR044 X11BR080 X13BR009 X01BR031 X06BR014 X01BR009 X11BR009 X11BR003 X01BR001 X11BR006 X11BR004 X11BR011 X21BR001 X14BR014 X21BR002 X01BR008 X11BR010 X18BR007 X11BR019 X11BR018 X18BR017 X11BR015 X11BR014 X11BR017 X11BR016 X01BR032 X01BR033 X01BR030 X11BR012 X11BR013
data/cBioPortal/brca_cptac_2020/case_lists/cases_phosphoprotein_quantification.txt ADDED
@@ -0,0 +1,5 @@
 
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ stable_id: brca_cptac_2020_phosphoprotein_quantification
3
+ case_list_name: Samples with phosphoprotein quantification data
4
+ case_list_description: Samples with phosphoprotein quantification data by mass spectrometry (122 samples)
5
+ case_list_ids: CPT000814 CPT001846 X01BR001 X01BR008 X01BR009 X01BR010 X01BR015 X01BR017 X01BR018 X01BR020 X01BR023 X01BR025 X01BR026 X01BR027 X01BR030 X01BR031 X01BR032 X01BR033 X01BR040 X01BR042 X01BR043 X03BR002 X03BR004 X03BR005 X03BR006 X03BR010 X03BR011 X03BR013 X05BR001 X05BR003 X05BR004 X05BR005 X05BR009 X05BR016 X05BR026 X05BR029 X05BR038 X05BR042 X05BR043 X05BR044 X05BR045 X06BR003 X06BR005 X06BR006 X06BR014 X09BR001 X09BR004 X09BR005 X09BR007 X11BR003 X11BR004 X11BR006 X11BR009 X11BR010 X11BR011 X11BR012 X11BR013 X11BR014 X11BR015 X11BR016 X11BR017 X11BR018 X11BR019 X11BR020 X11BR022 X11BR023 X11BR024 X11BR025 X11BR027 X11BR028 X11BR030 X11BR031 X11BR032 X11BR036 X11BR038 X11BR040 X11BR042 X11BR043 X11BR044 X11BR047 X11BR049 X11BR050 X11BR051 X11BR053 X11BR054 X11BR055 X11BR056 X11BR058 X11BR059 X11BR060 X11BR072 X11BR073 X11BR074 X11BR075 X11BR080 X13BR009 X14BR005 X14BR008 X14BR014 X15BR003 X16BR012 X18BR002 X18BR003 X18BR004 X18BR006 X18BR007 X18BR009 X18BR010 X18BR016 X18BR017 X18BR019 X20BR001 X20BR002 X20BR005 X20BR006 X20BR007 X20BR008 X21BR001 X21BR002 X21BR010 X22BR005 X22BR006
data/cBioPortal/brca_cptac_2020/case_lists/cases_protein_quantification.txt ADDED
@@ -0,0 +1,6 @@
 
 
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ stable_id: brca_cptac_2020_protein_quantification
3
+ case_list_name: Samples with protein data (Mass Spec)
4
+ case_list_description: Samples with protein data (Mass Spec) (122 samples)
5
+ case_list_category: other
6
+ case_list_ids: X14BR008 X14BR005 X01BR020 X01BR023 X01BR025 X15BR003 X01BR027 X01BR026 X22BR005 X22BR006 X11BR060 X01BR018 X05BR016 X18BR016 CPT000814 X18BR010 X18BR019 X11BR073 X11BR072 X11BR075 X11BR074 X18BR009 X05BR005 X05BR004 X05BR003 X05BR001 X09BR004 X18BR003 X18BR002 X18BR004 X05BR009 X18BR006 X01BR043 X01BR042 X01BR040 X11BR049 X11BR047 X11BR044 X11BR042 X11BR043 X11BR040 X20BR006 X20BR007 X20BR005 X20BR002 X20BR001 X20BR008 X11BR051 X11BR050 X11BR053 X11BR055 X11BR054 X11BR056 X11BR059 X11BR058 X16BR012 X09BR001 CPT001846 X09BR007 X03BR013 X03BR010 X03BR011 X09BR005 X11BR024 X11BR025 X05BR038 X11BR027 X11BR020 X11BR022 X11BR023 X11BR028 X03BR002 X03BR005 X03BR004 X03BR006 X06BR006 X06BR005 X06BR003 X01BR010 X01BR015 X01BR017 X11BR036 X05BR029 X11BR032 X11BR031 X11BR030 X05BR026 X11BR038 X05BR043 X05BR042 X21BR010 X05BR045 X05BR044 X11BR080 X13BR009 X01BR031 X06BR014 X01BR009 X11BR009 X11BR003 X01BR001 X11BR006 X11BR004 X11BR011 X21BR001 X14BR014 X21BR002 X01BR008 X11BR010 X18BR007 X11BR019 X11BR018 X18BR017 X11BR015 X11BR014 X11BR017 X11BR016 X01BR032 X01BR033 X01BR030 X11BR012 X11BR013
data/cBioPortal/brca_cptac_2020/case_lists/cases_sequenced.txt ADDED
@@ -0,0 +1,6 @@
 
 
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ stable_id: brca_cptac_2020_sequenced
3
+ case_list_name: Samples with mutation data
4
+ case_list_description: Samples with mutation data (122 samples)
5
+ case_list_category: all_cases_with_mutation_data
6
+ case_list_ids: X14BR008 X14BR005 X01BR020 X01BR023 X01BR025 X15BR003 X01BR027 X01BR026 X22BR005 X22BR006 X11BR060 X01BR018 X05BR016 X18BR016 X18BR017 X18BR010 X18BR019 X11BR073 X11BR072 X11BR075 X11BR074 X18BR009 X09BR001 X05BR004 X05BR003 X09BR005 X09BR004 X18BR003 X18BR002 X18BR004 X18BR007 X18BR006 X01BR043 X01BR042 X01BR040 X11BR049 X11BR047 X11BR044 X11BR042 X11BR043 X11BR040 X20BR006 X20BR007 X20BR005 X20BR002 X20BR001 X20BR008 X11BR051 X11BR050 X11BR053 X11BR055 X11BR054 X11BR056 X11BR059 X11BR058 X16BR012 X05BR005 CPT001846 X09BR007 X03BR013 X03BR010 X03BR011 X05BR001 X11BR024 X11BR025 X05BR038 X11BR027 X11BR020 X11BR022 X11BR023 X11BR028 X03BR002 X03BR005 X05BR009 X03BR006 X06BR006 X06BR005 X06BR003 X01BR010 X01BR015 X01BR017 X11BR036 X05BR029 X11BR032 X11BR031 X11BR030 X05BR026 X11BR038 X05BR043 X05BR042 X21BR010 X05BR045 X05BR044 X11BR080 X13BR009 X11BR012 X06BR014 X01BR009 X01BR008 X11BR003 X01BR001 X11BR006 X11BR004 X11BR011 X21BR001 X14BR014 X21BR002 X11BR009 X11BR010 X11BR019 X11BR018 CPT000814 X11BR015 X11BR014 X11BR017 X11BR016 X01BR032 X01BR033 X01BR030 X01BR031 X11BR013 X03BR004
data/cBioPortal/brca_cptac_2020/data_acetylprotein_quantification.txt ADDED
The diff for this file is too large to render. See raw diff
 
data/cBioPortal/brca_cptac_2020/data_clinical_patient.txt ADDED
@@ -0,0 +1,127 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ #Patient Identifier Age Sex Ethnicity ER Updated Clinical Status PR Clinical Status ERBB2 Updated Clinical Status TNBC Updated Clinical Status ERBB2 Proteogenomic Status TOP2A Proteogenomic Status ERBB2 Gene Amplified TOP2A Gene Amplified ESTIMATE TumorPurity CIBERSORT Absolute Score ESTIMATE Immune Score xCell Immune Score ESTIMATE Stromal Score xCell Stromal Score CD3 TILS Status CD3 TILS Counts APOBEC Signature Number of non synonymous Mutations Chromosome INstability index CIN Stemness Score
2
+ #Patient Identifier Age Sex Ethnicity Updated clinical ER status (central IHC for 68 tumors) Initial clinical PR status Updated clinical ERRB2 status (central IHC for 68 tumors) Triple Negative Breast Cancer (TNBC) status; based on PG ERBB2, updated clinical ER status; initial clinical PR status Proteogenomic ERBB2 status: gene copy amflification and outlier protein expression Proteogenomic TOP2A status: gene copy amflification and outlier protein expression Significant gene copy number amplification; based on GISTIC2 calls: thresholded == 2 & continuous > 1 Significant gene copy number amplification; based on GISTIC2 calls: thresholded == 2 & continuous > 1 Tumor purity inferred from mRNA using the ESTIMATE algorithm Level of immune cells inferred from mRNA using the CIBERSORT algorithm Level of immune infiltration inferred from mRNA using the ESTIMATE algorithm Level of immune cells inferred from mRNA using the xCell algorithm Level of stromal cells inferred from mRNA using the ESTIMATE algorithm Level of stromal cells inferred from mRNA using the xCell algorithm CD3 tumor-infiltrating lymphocytes (TILS) status. CD3+ cell counts Enriched APOBEC signature Total number of somatic mutations (non-synonymous) in the sample Chromosome instability index as genome wide measure for copy number alterations Stem cell-like phenotype score
3
+ #STRING NUMBER STRING STRING STRING STRING STRING STRING STRING STRING NUMBER NUMBER NUMBER NUMBER NUMBER NUMBER NUMBER NUMBER STRING STRING STRING NUMBER NUMBER NUMBER
4
+ #1 1 1 5 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 5 1
5
+ PATIENT_ID AGE SEX ETHNICITY ER_UPDATED_CLINICAL_STATUS PR_CLINICAL_STATUS ERBB2_UPDATED_CLINICAL_STATUS TNBC_UPDATED_CLINICAL_STATUS ERBB2_PROTEOGENOMIC_STATUS TOP2A_PROTEOGENOMIC_STATUS ERBB2_GENE_AMPLIFIED TOP2A_GENE_AMPLIFIED ESTIMATE_TUMORPURITY CIBERSORT_ABSOLUTE_SCORE ESTIMATE_IMMUNE_SCORE XCELL_IMMUNE_SCORE ESTIMATE_STROMAL_SCORE XCELL_STROMAL_SCORE CD3_TILS_STATUS CD3_TILS_COUNTS APOBEC_SIGNATURE NUMBER_OF_NON_SYNONYMOUS_MUTATIONS CHROMOSOME_INSTABILITY_INDEX_CIN_ STEMNESS_SCORE
6
+ CPT000814 NA NA Black or African American Negative negative NA Positive Negative negative 0 0 0.819666 0.565019 846.350897 0.0414 -812.409581 0 not performed not performed N 92 2.2719461 0.798050042
7
+ CPT001846 NA NA White Negative negative NA Positive Negative negative 0 0 0.631766 0.785537 1425.391899 0.0766 495.60375 0.0236 not performed not performed N 80 0.826617402 0.59210011
8
+ X01BR001 55 Female Black or African American Negative negative Negative Positive Negative negative 0 0 0.822598 0.45449 475.804314 0.0103 -476.863678 0.0088 not performed not performed N 79 1.137608521 0.839482756
9
+ X01BR008 NA NA NA NA NA NA NA Negative negative 0 0 0.535194 2.064309 2809.59164 0.484 -77.281727 0.0033 not performed not performed N 128 0.466991648 0.599871203
10
+ X01BR009 NA NA NA Negative negative NA Positive Negative negative 0 0 0.576875 1.191462 1664.85538 0.0926 725.73435 0.0265 not performed not performed N 129 4.30213853 0.437721346
11
+ X01BR010 NA NA NA Negative negative NA Positive Negative negative 0 0 0.755079 0.498983 375.355547 0.0155 374.25274 0.0352 T 60 N 88 0.456320974 0.514976271
12
+ X01BR015 35 Female White Positive positive Negative negative Negative negative 0 0 0.668922 0.720781 1119.306238 0.0638 468.365511 0.043 not performed not performed N 55 1.379587319 0.644329816
13
+ X01BR017 45 Female White Negative negative Positive Negative Positive Negative 1 0 0.564613 1.272618 1883.327193 0.1311 608.997993 0.0202 not performed not performed N 134 1.060969462 0.790127929
14
+ X01BR018 66 Female White Positive Negative negative Negative negative Negative 0 0 0.522033 1.66713 2247.377844 0.2108 590.562586 0.0245 not performed not performed N 324 6.068239982 0.763500408
15
+ X01BR020 NA NA NA Negative negative NA Positive Negative negative 0 0 0.653076 1.290331 1685.766454 0.146 45.776067 0.0094 not performed not performed N 93 4.220512167 0.761221232
16
+ X01BR023 NA NA NA Positive positive equivocal Negative negative Negative 0 0 0.957035 0.152146 -676.347021 0.0114 -1440.910847 0.0053 T 5 N 36 3.897837169 0.503055849
17
+ X01BR025 62 Female Black or African American Positive positive equivocal Negative negative Negative 0 0 0.799688 0.316919 644.717853 0.0789 -378.799768 0 T 45 NA 12 0.477414509 0.618749629
18
+ X01BR026 NA NA White Negative negative NA Positive Negative negative 0 0 0.395393 1.574962 2231.321092 0.1655 1579.015155 0.0876 not performed not performed N 79 1.758586002 0.3457811
19
+ X01BR027 80 Female Black or African American Negative negative Negative Positive Negative negative 0 0 0.804447 0.534953 616.765017 0.0603 -405.13497 0 T 55 N 186 1.842240206 0.994348097
20
+ X01BR030 84.16666667 Female Black or African American Positive positive Negative negative Negative negative 0 0 0.514312 1.607262 2544.70288 0.3263 354.735906 0.0078 T 50 N 71 0.650297221 0.403733619
21
+ X01BR031 61.66666667 Female Black or African American Negative negative NA Positive Negative negative 0 0 0.686517 0.88796 1061.244615 0.0442 363.401402 0.032 not performed not performed N 56 2.547830638 0.901913474
22
+ X01BR032 46.41666667 Female White Positive positive Negative negative Negative negative 0 0 0.900993 0.210575 -215.651386 0.0059 -848.767325 0.0008 not performed not performed N 30 1.113350459 0.519343598
23
+ X01BR033 40.41666667 Female Black or African American Positive positive Negative negative Negative negative 0 0 0.563018 0.991935 1559.912463 0.0765 945.572025 0.0631 not performed not performed N 96 3.055750677 0.609263714
24
+ X01BR040 NA NA Black or African American Negative negative NA Positive Negative negative 0 0 0.553952 1.465522 2369.41481 0.2647 210.526322 0.0039 not performed not performed N 45 1.571783285 0.794146359
25
+ X01BR042 NA NA Black or African American Negative negative NA Positive Negative negative 0 0 0.72903 0.992146 1712.974756 0.1451 -698.551999 0.001 not performed not performed N 101 4.495325229 0.727150988
26
+ X01BR043 NA NA White Negative negative NA Positive Negative negative 0 0 0.652287 1.698384 2200.849893 0.1844 -462.212213 0 not performed not performed N 8705 2.925318968 0.756322946
27
+ X03BR002 60.58333333 Female White Positive positive Negative negative Negative negative 0 0 0.743671 0.499958 500.233532 0.0106 366.762223 0.0088 not performed not performed N 30 0.263150091 0.431648131
28
+ X03BR004 88.66666667 Female White Positive positive Negative negative Negative negative 0 0 0.730184 0.492183 374.456365 0.0346 628.472482 0.1365 not performed not performed N 54 0.448071755 0.519619952
29
+ X03BR005 61.5 Female White Positive positive Negative negative Negative negative 0 0 0.598417 0.809317 1023.633109 0.0194 1185.566943 0.3498 not performed not performed NA 14 0.053447784 0.29181424
30
+ X03BR006 NA NA White Negative negative NA Positive Negative negative 0 0 0.770509 0.746765 917.34243 0.0525 -330.308601 0.0012 not performed not performed N 98 5.661405304 0.597843423
31
+ X03BR010 78.58333333 Female White Positive positive Negative negative Negative negative 0 0 0.830292 0.292846 289.720214 0.0079 -383.884193 0.0078 not performed not performed N 60 1.257480784 0.481619351
32
+ X03BR011 NA NA White Positive Negative NA Negative negative Negative 0 0 0.774357 0.451309 473.421364 0.017 72.337367 0.0092 not performed not performed N 50 0.390927321 0.53724318
33
+ X03BR013 52.16666667 Female NA Positive positive Negative negative Negative negative 0 0 0.615701 1.116004 1339.959919 0.0776 721.056076 0.0948 not performed not performed N 39 1.43545494 0.57002901
34
+ X05BR001 70 Female White Negative Positive Negative negative Negative negative 0 0 0.36873 1.690603 2756.194524 0.2853 1250.704619 0.0606 T 70 N 33 0.119783512 0.640608263
35
+ X05BR003 37.58333333 Female White Positive positive Negative negative Negative negative 0 0 0.608072 0.97308 1118.583239 0.0493 1008.147388 0.2267 T 45 N 72 1.822497393 0.390987945
36
+ X05BR004 NA NA White Positive positive NA Negative negative Negative 0 0 0.726689 0.677208 656.337828 0.0163 381.338096 0.0804 not performed not performed N 62 0.942026652 0.183419141
37
+ X05BR005 50 Female White Positive positive Negative negative Negative negative 0 0 0.692142 0.40252 508.65917 0.0264 863.091214 0.055 PT 20 N 74 1.48710105 0.422111675
38
+ X05BR009 64.33333333 Female White Positive positive Negative negative Negative negative 0 0 0.51536 1.080917 1300.544501 0.0447 1590.568417 0.1984 not performed not performed N 102 0.255161644 0.272647335
39
+ X05BR016 78.16666667 Female White Positive positive Negative negative Negative negative 0 0 0.808678 0.319954 244.42179 0.0479 -81.547065 0.0026 PT 25 N 80 0.171408231 0.49930901
40
+ X05BR026 71.5 Female White Positive positive Positive Negative Positive Negative 1 0 0.419537 1.243373 2072.995491 0.0821 1557.223982 0.1918 T 40 N 38 1.224621802 0.486667428
41
+ X05BR029 61.91666667 Female White Negative negative Negative Positive Negative negative 0 0 0.800564 0.770379 1276.678004 0.0841 -1020.703611 0 T 80 N 393 4.036541722 0.900263956
42
+ X05BR038 52.25 Female White Positive positive Negative negative Negative negative 0 0 0.689659 0.824787 771.383893 0.0279 623.762794 0.0213 PT 45 Y 408 0.765850842 0.506482396
43
+ X05BR042 40 Female White Negative negative Negative Positive Negative negative 0 0 0.6892 1.060131 1586.64542 0.0601 -187.183541 0.007 PT 70 N 130 2.467613128 0.831125808
44
+ X05BR043 50 Female White Negative negative Negative Positive Negative negative 0 0 0.635422 1.241093 1641.832908 0.0957 246.970721 0.0011 T 60 N 156 3.979357879 0.738955715
45
+ X05BR044 62.75 Female White Positive Negative negative Negative negative Negative 0 0 0.739732 0.688107 958.975 0.0636 -51.971406 0.0102 PT 10 N 56 0.738050003 0.392150606
46
+ X05BR045 60 Female White Negative negative equivocal Positive Negative negative 0 0 0.775181 0.816303 996.747694 0.0223 -459.868422 0.0107 T 30 N 72 3.525720695 0.615236356
47
+ X06BR003 75 Female Hispanic or Latino Positive Negative equivocal Negative negative Positive 1 1 0.633125 0.987732 1397.369991 0.1502 511.668718 0.0016 not performed not performed N 121 1.130305284 0.653817719
48
+ X06BR005 58 Female Hispanic or Latino Positive positive equivocal Negative negative Negative 0 0 0.684447 0.861046 1216.147841 0.0647 227.860575 0.013 not performed not performed N 64 0.655766629 0.545120343
49
+ X06BR006 51 Female Hispanic or Latino Negative negative equivocal Negative Positive Negative 1 0 0.50625 0.882338 1442.230636 0.0071 1521.072943 0.3597 not performed not performed NA 109 0.158407665 0.45327286
50
+ X06BR014 51 Female Hispanic or Latino Positive positive Negative negative Negative negative 0 0 0.816296 0.463028 166.427034 0.0216 -92.580645 0.0096 not performed not performed N 28 1.117140342 0.479834639
51
+ X09BR001 NA NA NA Positive positive NA Negative negative Negative 0 0 0.789744 0.299912 678.901475 0.0303 -301.366779 0.0016 not performed not performed N 57 1.506875662 0.163424541
52
+ X09BR004 75.33333333 Female White Positive positive Positive Negative Positive positive 1 1 0.937017 0.286701 -668.551236 0.0141 -1022.189811 0.0296 not performed not performed NA 64 2.4659498 0.75219565
53
+ X09BR005 38.25 Female White Positive positive Positive Negative Positive positive 1 1 0.7839 0.27765 149.666807 0.013 292.376028 0.0005 not performed not performed N 83 1.980462775 0.829954222
54
+ X09BR007 77.5 Female White Positive positive Positive Negative negative Negative 0 0 0.649722 0.890766 1379.805113 0.0642 381.84552 0.0462 not performed not performed N 55 0.954156191 0.552216509
55
+ X11BR003 53.58333333 Female Asian Negative negative Negative Positive Negative negative 0 0 0.522455 1.820174 2713.222395 0.4051 121.34361 0 not performed not performed N 881 0.501259382 0.946462569
56
+ X11BR004 54.5 Female Asian Positive positive Positive Negative Positive Negative 1 0 0.511529 2.018323 2426.051879 0.2778 495.473287 0.0089 T 75 N 47 0.789010588 0.611965455
57
+ X11BR006 54.5 Female Asian Positive positive Negative negative Negative negative 0 0 0.65171 0.950416 1324.834522 0.0841 418.982014 0.079 NT 0 N 89 1.602702501 0.658172466
58
+ X11BR009 44.16666667 Female Asian Positive positive Negative negative Negative negative 0 0 0.781986 0.863016 1029.908175 0.0569 -566.90084 0.0058 T 50 N 139 4.273306928 0.560365573
59
+ X11BR010 35.58333333 Female Asian Positive positive Positive Negative Positive Negative 1 0 0.60255 0.955077 1353.971531 0.0563 820.015466 0.0171 T 50 N 52 1.415629832 0.522933472
60
+ X11BR011 71.5 Female Asian Positive positive equivocal Negative Positive Negative 1 1 0.524123 1.408118 2187.725322 0.2124 633.504183 0.0703 T 60 N 45 1.061994048 0.592100237
61
+ X11BR012 77 Female White Positive Negative negative Negative negative Negative 0 0 0.753768 0.554932 838.54153 0.0475 -75.321046 0.005 PT 5 N 105 2.63410438 0.54414769
62
+ X11BR013 70 Female White Positive Negative negative Negative negative Negative 0 0 0.802188 0.505907 492.568589 0.015 -255.099747 0.0806 T 15 N 67 0.942759279 0.644401762
63
+ X11BR014 39.66666667 Female White Positive positive Negative negative Negative negative 0 0 0.505997 1.000703 1458.02589 0.0313 1507.273907 0.0692 T 10 N 83 0.072014552 0.436756036
64
+ X11BR015 60 Female White Positive Negative negative Negative negative Negative 0 0 0.876341 0.338225 -22.733317 0.0235 -674.887898 0.0114 PT 10 N 30 1.373961288 0.65731941
65
+ X11BR016 30.91666667 Female White Negative negative Negative Positive Negative negative 0 0 0.727575 1.369973 1486.399787 0.0694 -457.511032 0 T 70 N 80 1.96930412 1
66
+ X11BR017 74.75 Female White Negative negative Negative Positive Negative negative 0 0 0.651856 1.090942 1639.612214 0.1133 102.893143 0.0112 T 60 N 56 1.084218653 0.558870506
67
+ X11BR018 54.41666667 Female White Positive positive Negative negative Negative negative 0 0 0.452693 1.547491 2091.740653 0.1287 1287.446874 0.1968 T 45 N 73 0.167410177 0.337389506
68
+ X11BR019 61.25 Female White Positive positive Negative negative Negative negative 1 0 0.69222 1.04273 1719.617176 0.309 -348.606579 0.0088 T 70 N 98 1.485021635 0.576993504
69
+ X11BR020 37.5 Female White Positive positive Negative negative Negative negative 0 0 0.599275 1.319588 1725.041825 0.0804 476.866338 0.0686 T 40 N 129 1.349644706 0.627061119
70
+ X11BR022 48.66666667 Female White Positive positive Negative negative Negative negative 0 0 0.701999 0.796172 893.021712 0.0419 385.068534 0.0094 T 25 N 54 0.041769587 0.68522813
71
+ X11BR023 58.5 Female White Negative negative Negative Positive Negative negative 0 0 0.58525 1.416804 2056.103037 0.1475 264.384302 0 T 30 N 110 1.015638905 0.835644026
72
+ X11BR024 80.75 Female White Negative negative Negative Positive Negative negative 0 0 0.621099 1.488928 2238.743018 0.1537 -224.520717 0 T 65 N 88 1.371127518 0.780612324
73
+ X11BR025 77.41666667 Female White Positive positive Negative negative Negative negative 0 0 0.896845 0.233066 -289.516909 0.0079 -710.395533 0.002 PT 5 N 53 0.099965473 0.55287122
74
+ X11BR027 76.16666667 Female White Positive positive Negative negative Negative negative 0 0 0.713649 0.822915 1279.40903 0.0596 -113.677851 0.0014 PT 25 N 125 0.882946157 0.363530924
75
+ X11BR028 55.33333333 Female White Negative negative Positive Negative Positive Negative 1 0 0.735588 0.463925 791.509885 0.0479 157.302638 0.0079 T 40 N 104 3.160146832 0.775925119
76
+ X11BR030 50.75 Female Asian Negative negative Positive Negative Positive Negative 1 0 0.471635 1.617953 2765.526834 0.3322 468.139173 0.031 PT 15 Y 95 0.394085544 0.647774985
77
+ X11BR031 50 Female Asian Positive positive Negative negative Negative negative 0 0 0.582517 1.008895 1519.115732 0.0783 824.303566 0.0836 T 35 Y 377 1.76392698 0.472024607
78
+ X11BR032 49.75 Female Asian Positive positive Negative negative Negative negative 0 0 0.565583 1.079728 1337.777641 0.0367 1146.538057 0.1185 T 5 N 19 0.307859209 0.45262614
79
+ X11BR036 51.58333333 Female Asian Negative negative Negative Positive Negative negative 0 0 0.897906 0.234612 -73.398721 0.0051 -942.899492 0.0064 PT 5 N 67 2.126255904 0.832424603
80
+ X11BR038 47.41666667 Female Asian Negative NA Positive Negative Positive Negative 1 0 0.54121 2.000247 2208.369097 0.369 475.316791 0.0363 PT 30 N 44 0.606024653 0.651021466
81
+ X11BR040 67.83333333 Female Asian Positive positive Negative negative Negative negative 0 0 0.742148 0.67328 716.550157 0.0229 165.941259 0.0666 T 20 N 32 0.265259668 0.427947648
82
+ X11BR042 71.41666667 Female White Negative negative Negative Positive Negative negative 0 0 0.701389 0.702472 934.889391 0.0527 349.034868 0.0158 T 30 N 31 0.73203768 0.640158289
83
+ X11BR043 36.66666667 Female White Positive positive Negative negative Negative negative 0 0 0.53396 1.434464 2288.081121 0.2159 454.178235 0.001 T 70 N 83 2.715802638 0.722097264
84
+ X11BR044 48 Female White Positive positive Negative negative Negative negative 0 0 0.711318 1.058189 1127.109032 0.1125 61.254668 0.0056 T 60 N 54 1.91595668 0.830750536
85
+ X11BR047 59.16666667 Female Asian Positive positive Negative negative Negative negative 0 0 0.71902 0.636493 635.421797 0.0555 477.871345 0.0248 T 50 N 29 0.630788376 0.527025208
86
+ X11BR049 45.83333333 Female Asian Positive positive Negative negative Negative negative 0 0 0.674546 1.139219 1242.772843 0.0585 293.173402 0.0089 T 65 N 79 1.388772689 0.622909634
87
+ X11BR050 54 Female Asian Positive positive Negative negative Negative negative 0 0 0.493014 1.18295 1590.251314 0.0525 1477.145666 0.2123 PT 10 N 28 0.121141789 0.453744928
88
+ X11BR051 65.41666667 Female White Positive positive Negative negative Negative negative 0 0 0.652469 0.815085 1211.405372 0.0605 525.588902 0.0462 T 15 N 45 1.361058459 0.487273371
89
+ X11BR053 61.91666667 Female White Positive positive Negative negative Negative negative 0 0 0.829248 0.40404 201.171392 0.0251 -282.591904 0.0043 PT 10 N 82 3.656801476 0.573902251
90
+ X11BR054 84.41666667 Female White Positive positive Negative negative Negative negative 0 0 0.869544 0.329558 101.496162 0.037 -704.19923 0 T 35 N 26 0.026149142 0.441018246
91
+ X11BR055 56.25 Female White Positive positive Negative negative Negative negative 0 0 0.599412 0.818386 1107.703403 0.0361 1093.033872 0.0626 T 5 N 85 1.555005308 0.61919958
92
+ X11BR056 52.83333333 Female Asian Positive Negative negative Negative negative Negative 0 0 0.557649 1.21051 1629.27314 0.1494 920.369961 0.0644 T 70 N 39 1.800882719 0.581368778
93
+ X11BR058 65.58333333 Female Asian Negative NA Negative NA Negative negative 0 0 0.554292 0.873502 1372.43086 0.1061 1204.728316 0.0498 T 10 NA 63 1.010827695 0.585720082
94
+ X11BR059 45.91666667 Female Asian Positive NA Negative negative Negative negative 0 0 0.711566 1.001855 1052.949848 0.0141 133.006864 0.0093 T 60 NA 70 0.812461627 0.743880292
95
+ X11BR060 52.83333333 Female Asian Negative negative Positive Negative Positive positive 1 1 0.595905 0.903779 1265.591305 0.0727 964.948681 0.0298 T 55 N 117 4.033835805 0.602351578
96
+ X11BR072 70.66666667 Female White Positive positive Negative negative Negative negative 0 0 0.658547 0.79744 1076.824162 0.0308 605.341579 0.145 T 50 N 46 0.133328699 0.395994083
97
+ X11BR073 64.58333333 Female White Positive positive Negative negative Negative negative 0 0 0.526436 1.568457 2565.542979 0.3263 237.171381 0.0026 T 75 N 82 1.468737918 0.64934993
98
+ X11BR074 66.16666667 Female White Positive positive Negative negative Negative negative 0 0 0.614957 0.860188 991.831168 0.0252 1075.616092 0.0394 T 10 N 20 0.310636112 0.50579834
99
+ X11BR075 79.41666667 Female White Positive NA Negative negative Negative negative 0 0 0.687257 0.770334 954.540245 0.0515 463.164821 0.0274 T 30 N 166 3.39840801 0.624065815
100
+ X11BR080 68.33333333 Female White Positive positive Negative negative Negative negative 0 0 0.552769 1.593937 2255.776041 0.2532 333.844739 0.0125 T 55 N 71 1.451119883 0.826384301
101
+ X13BR009 75 Female White Positive positive Negative negative Negative negative 0 0 0.800117 0.49338 503.860612 0.0283 -242.807701 0.0286 not performed not performed N 70 2.826122978 0.660835387
102
+ X14BR005 78.33333333 Female White Positive positive NA Negative negative Negative 0 0 0.802282 0.535901 634.281663 0.0449 -397.879373 0.0149 not performed not performed N 39 1.677906218 0.526800316
103
+ X14BR008 66.33333333 Female White Positive positive Negative negative Negative negative 0 0 0.571791 0.984642 1243.442351 0.0216 1189.459127 0.2005 not performed not performed N 25 0.29960095 0.313464221
104
+ X14BR014 59.16666667 Female White Positive positive Negative negative Negative negative 0 0 0.707649 0.87434 700.860825 0.0451 522.965467 0.1019 not performed not performed N 23 0.202887753 0.458240632
105
+ X15BR003 74.58333333 Female White Positive Negative negative Negative negative Negative 0 0 0.583488 1.238836 1556.414992 0.1377 778.866509 0.1262 not performed not performed Y 711 0.139798332 0.297940894
106
+ X16BR012 47.5 Female White NA NA NA NA Negative negative 0 0 0.727713 0.578108 590.628133 0.0393 436.886485 0.0438 not performed not performed Y 170 0.793115717 0.667343261
107
+ X18BR002 64.08333333 Female White Negative negative Negative Positive Negative negative 0 0 0.4172 1.383812 2206.669318 0.1023 1441.074516 0.0326 T 5 N 158 1.164432244 0.501459032
108
+ X18BR003 65.83333333 Female White Positive Negative negative Negative negative Negative 0 0 0.647554 1.35861 1853.547775 0.1408 -72.486852 0.0032 T 60 Y 1066 0.572258451 0.568389356
109
+ X18BR004 76.75 Female White Positive positive Negative negative Negative negative 0 0 0.85359 0.404123 57.675786 0.0313 -446.188976 0.0089 NT 1 N 28 0.374702641 0.508861174
110
+ X18BR006 62.33333333 Female White Positive positive Negative negative Negative negative 0 0 0.574355 0.919271 1428.845476 0.0655 982.740632 0.0777 PT 5 N 131 3.248566526 0.606374976
111
+ X18BR007 64 Female White Positive positive equivocal Negative negative Negative 0 0 0.616992 0.95944 1445.219269 0.0672 604.632201 0.005 not performed not performed N 102 1.238151274 0.628674444
112
+ X18BR009 63.5 Female White Negative negative Positive Negative Positive Negative 1 0 0.472941 1.918183 2385.70268 0.3099 837.874347 0.0992 PT 70 NA 64 0.459675173 0.496640158
113
+ X18BR010 41 Female White Positive positive Negative negative Negative negative 0 0 0.634357 0.784446 966.576375 0.0462 931.613195 0.0266 PT 10 N 28 0.519579637 0.671878422
114
+ X18BR016 73.75 Female White Positive NA Negative negative Negative negative 0 0 0.698784 0.510331 537.772533 0.0173 771.005706 0.0438 PT 1 N 36 0.739682923 0.438941735
115
+ X18BR017 72.66666667 Female White Positive Negative negative Negative negative Negative 0 0 0.602272 1.082374 1304.195032 0.0873 872.169912 0.0206 not performed not performed N 82 1.802915153 0.56306069
116
+ X18BR019 68.08333333 Female White Positive positive Negative negative Negative negative 0 0 0.727492 0.683072 838.600703 0.0137 191.107936 0.0523 not performed not performed N 31 0.323082858 0.431888007
117
+ X20BR001 82.16666667 Female Black or African American Positive positive Negative negative Negative negative 0 0 0.699324 0.63872 1240.694726 0.1175 62.931282 0 not performed not performed N 36 0.758862705 0.318753217
118
+ X20BR002 95.33333333 Female White Negative Positive Negative negative Negative negative 0 0 0.707173 0.643153 680.311661 0.0289 548.100456 0.0389 not performed not performed N 115 2.420805736 0.779723581
119
+ X20BR005 47.33333333 Female Black or African American Negative negative Negative Positive Negative negative 0 0 0.654655 0.526494 932.987215 0.0393 784.333896 0.001 not performed not performed N 139 3.97560851 0.553935398
120
+ X20BR006 65.5 Female White Positive Negative negative Negative negative Negative 0 0 0.775527 0.339632 535.17001 0.0059 -2.021472 0.0059 not performed not performed N 96 2.879015576 0.451417647
121
+ X20BR007 55 Female Black or African American Negative negative Negative Positive Negative negative 0 0 0.588594 0.731444 1507.621871 0.1303 784.728836 0 not performed not performed N 129 2.437907928 0.526077873
122
+ X20BR008 71.91666667 Female Black or African American Negative negative Negative Positive Negative negative 0 0 0.610224 0.385938 954.860667 0.0747 1153.385721 0.0095 not performed not performed N 94 0.26096968 0.183250787
123
+ X21BR001 NA NA White Negative negative NA Negative Positive Negative 1 0 0.625141 1.085131 2014.358538 0.1573 -35.342048 0.004 not performed not performed N 287 1.925994132 0.356451504
124
+ X21BR002 NA NA White Positive positive NA Negative negative Negative 0 0 0.543167 0.959089 1956.58573 0.1577 711.234125 0.0136 not performed not performed N 50 0.751422632 0.263091541
125
+ X21BR010 71 Female White Positive positive Negative negative Negative negative 0 0 0.682815 0.267234 628.877273 0.0293 830.372368 0.0195 not performed not performed N 26 0.345134879 0
126
+ X22BR005 46 Female White Positive positive Positive Negative Positive Negative 1 0 0.674586 1.010303 1346.716615 0.0647 188.859577 0.004 not performed not performed N 98 1.722306367 0.605869428
127
+ X22BR006 55 Female Black or African American Positive positive Negative negative Negative negative 0 0 0.67507 0.890611 1012.34597 0.0553 518.765898 0.0768 not performed not performed N 21 0.381897508 0.411004451
data/cBioPortal/brca_cptac_2020/data_clinical_sample.txt ADDED
@@ -0,0 +1,127 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ #Patient Identifier Sample Identifier Cancer type Cancer Type Detailed Ischemia Time in Minutes NMF Cluster NMF Cluster Membership Score Oncotree code PAM50 TMT Channel TMT Plex Tumor Stage TMB (nonsynonymous)
2
+ #Patient Identifier Sample Identifier Cancer type Cancer Type Detailed Ischemia time in minutes NMF-based multi-omics subtype Cluster Membership score indicating the representiveness of a tumor in its cluster Oncotree code PAM50 classification TMT10 reporter ion channel TMT10 plex number Tumor stage TMB (nonsynonymous)
3
+ #STRING STRING STRING STRING NUMBER STRING NUMBER STRING STRING STRING STRING STRING NUMBER
4
+ #1 1 1 1 1 1 1 1 5 1 1 5 1
5
+ PATIENT_ID SAMPLE_ID CANCER TYPE CANCER_TYPE_DETAILED ISCHEMIA_TIME_IN_MINUTES NMF_CLUSTER NMF_CLUSTER_MEMBERSHIP_SCORE ONCOTREE CODE PAM50 TMT_CHANNEL TMT_PLEX TUMOR_STAGE TMB_NONSYNONYMOUS
6
+ CPT000814 CPT000814 Breast Cancer Invasive Breast Carcinoma NA Basal-I 1 BRCA Basal 127C 13 Stage IIA 2.7
7
+ CPT001846 CPT001846 Breast Cancer Invasive Breast Carcinoma NA Basal-I 0.672 BRCA Basal 128C 12 Stage III 2.46666666667
8
+ X01BR001 X01BR001 Breast Cancer Invasive Breast Carcinoma 0 Basal-I 0.782 BRCA Basal 129N 2 Stage IIB 2.4
9
+ X01BR008 X01BR008 Breast Cancer Invasive Breast Carcinoma NA Basal-I 0.958 BRCA Basal 127C 16 NA 4.03333333333
10
+ X01BR009 X01BR009 Breast Cancer Invasive Breast Carcinoma NA Basal-I 0.825 BRCA Basal 127N 16 NA 3.76666666667
11
+ X01BR010 X01BR010 Breast Cancer Invasive Breast Carcinoma NA HER2-I 0.734 BRCA Her2 130C 17 NA 2.6
12
+ X01BR015 X01BR015 Breast Cancer Invasive Breast Carcinoma 1 LumA-I 0.55 BRCA LumA 128N 2 Stage IIB 1.66666666667
13
+ X01BR017 X01BR017 Breast Cancer Invasive Breast Carcinoma 0 Basal-I 0.508 BRCA Her2 130C 1 Stage III 4.26666666667
14
+ X01BR018 X01BR018 Breast Cancer Invasive Breast Carcinoma 1 Basal-I 0.915 BRCA Basal 129N 7 Stage IIIA 10.3333333333
15
+ X01BR020 X01BR020 Breast Cancer Invasive Breast Carcinoma NA Basal-I 0.913 BRCA Basal 127C 17 NA 2.9
16
+ X01BR023 X01BR023 Breast Cancer Invasive Breast Carcinoma NA LumB-I 1 BRCA LumA 126 17 NA 1.1
17
+ X01BR025 X01BR025 Breast Cancer Invasive Breast Carcinoma 6 LumB-I 0.551 BRCA LumA 127N 9 Stage IIIA 0.366666666667
18
+ X01BR026 X01BR026 Breast Cancer Invasive Breast Carcinoma NA Basal-I 0.555 BRCA Basal 129N 16 NA 2.56666666667
19
+ X01BR027 X01BR027 Breast Cancer Invasive Breast Carcinoma 8 Basal-I 1 BRCA Basal 127N 3 Stage IIA 5.83333333333
20
+ X01BR030 X01BR030 Breast Cancer Invasive Breast Carcinoma 4 LumA-I 0.409 BRCA LumA 128C 7 Stage IIIA 2.13333333333
21
+ X01BR031 X01BR031 Breast Cancer Invasive Breast Carcinoma 9 Basal-I 0.816 BRCA Basal 130N 6 Stage III 1.66666666667
22
+ X01BR032 X01BR032 Breast Cancer Invasive Breast Carcinoma 0 LumB-I 0.854 BRCA LumB 130N 2 Stage IIIB 0.9
23
+ X01BR033 X01BR033 Breast Cancer Invasive Breast Carcinoma 10 LumA-I 0.634 BRCA LumA 128N 5 Stage III 3.0
24
+ X01BR040 X01BR040 Breast Cancer Invasive Breast Carcinoma NA Basal-I 0.938 BRCA Basal 127N 11 Stage IIB 1.4
25
+ X01BR042 X01BR042 Breast Cancer Invasive Breast Carcinoma NA Basal-I 0.99 BRCA Basal 128N 13 NA 3.06666666667
26
+ X01BR043 X01BR043 Breast Cancer Invasive Breast Carcinoma NA Basal-I 0.825 BRCA Basal 129C 9 NA 264.633333333
27
+ X03BR002 X03BR002 Breast Cancer Invasive Breast Carcinoma 15 LumA-I 0.6 BRCA LumA 126 12 Stage IIIA 0.933333333333
28
+ X03BR004 X03BR004 Breast Cancer Invasive Breast Carcinoma 24 LumA-I 0.559 BRCA LumA 130N 3 Stage IIB 1.7
29
+ X03BR005 X03BR005 Breast Cancer Invasive Breast Carcinoma 12 LumA-I 1 BRCA LumA 126 7 Stage IIA 0.4
30
+ X03BR006 X03BR006 Breast Cancer Invasive Breast Carcinoma NA Basal-I 0.93 BRCA Basal 130N 16 NA 3.16666666667
31
+ X03BR010 X03BR010 Breast Cancer Invasive Breast Carcinoma 21 LumB-I 0.791 BRCA LumA 129C 5 Stage IIA 1.93333333333
32
+ X03BR011 X03BR011 Breast Cancer Invasive Breast Carcinoma NA LumB-I 0.65 BRCA LumA 129C 17 NA 1.6
33
+ X03BR013 X03BR013 Breast Cancer Invasive Breast Carcinoma 9 LumA-I 0.779 BRCA LumA 128C 3 Stage IIA 1.23333333333
34
+ X05BR001 X05BR001 Breast Cancer Invasive Breast Carcinoma 29 HER2-I 0.586 BRCA Basal 128N 6 Stage IIB 0.966666666667
35
+ X05BR003 X05BR003 Breast Cancer Invasive Breast Carcinoma 30 LumA-I 0.781 BRCA LumA 130N 9 Stage IIB 2.3
36
+ X05BR004 X05BR004 Breast Cancer Invasive Breast Carcinoma NA LumA-I 0.535 BRCA LumA 129C 16 NA 1.73333333333
37
+ X05BR005 X05BR005 Breast Cancer Invasive Breast Carcinoma 11 LumA-I 0.607 BRCA LumA 130C 12 Stage IA 2.26666666667
38
+ X05BR009 X05BR009 Breast Cancer Invasive Breast Carcinoma 28 LumA-I 1 BRCA LumA 126 9 Stage IIIC 3.26666666667
39
+ X05BR016 X05BR016 Breast Cancer Invasive Breast Carcinoma 20 LumB-I 0.786 BRCA LumA 128N 7 Stage IIB 2.4
40
+ X05BR026 X05BR026 Breast Cancer Invasive Breast Carcinoma 19 LumA-I 0.683 BRCA LumA 127N 10 Stage IIA 1.13333333333
41
+ X05BR029 X05BR029 Breast Cancer Invasive Breast Carcinoma 13 Basal-I 0.898 BRCA Basal 130C 9 Stage IIA 11.7666666667
42
+ X05BR038 X05BR038 Breast Cancer Invasive Breast Carcinoma 22 LumA-I 0.598 BRCA LumA 128C 11 Stage IA 12.8
43
+ X05BR042 X05BR042 Breast Cancer Invasive Breast Carcinoma 20 Basal-I 1 BRCA Basal 129C 7 Stage IIB 4.2
44
+ X05BR043 X05BR043 Breast Cancer Invasive Breast Carcinoma 16 Basal-I 0.771 BRCA Basal 126 10 Stage IIB 4.93333333333
45
+ X05BR044 X05BR044 Breast Cancer Invasive Breast Carcinoma 17 HER2-I 0.863 BRCA Her2 126 8 Stage IIB 1.73333333333
46
+ X05BR045 X05BR045 Breast Cancer Invasive Breast Carcinoma 13 Basal-I 0.826 BRCA Basal 130C 2 Stage IIA 2.2
47
+ X06BR003 X06BR003 Breast Cancer Invasive Breast Carcinoma 11 HER2-I 0.333 BRCA Her2 129N 1 Stage IIA 3.76666666667
48
+ X06BR005 X06BR005 Breast Cancer Invasive Breast Carcinoma 15 LumB-I 0.604 BRCA LumA 129C 8 Stage IIA 1.9
49
+ X06BR006 X06BR006 Breast Cancer Invasive Breast Carcinoma 14 LumA-I 0.824 BRCA Normal-like 126 2 NA 3.5
50
+ X06BR014 X06BR014 Breast Cancer Invasive Breast Carcinoma 16 LumB-I 0.577 BRCA LumA 128N 12 Stage IIB 0.9
51
+ X09BR001 X09BR001 Breast Cancer Invasive Breast Carcinoma NA LumB-I 0.799 BRCA LumA 129N 17 NA 1.63333333333
52
+ X09BR004 X09BR004 Breast Cancer Invasive Breast Carcinoma 12 Basal-I 0.446 BRCA Normal-like 130N 11 Stage IIA 1.93333333333
53
+ X09BR005 X09BR005 Breast Cancer Invasive Breast Carcinoma 22 HER2-I 0.569 BRCA Her2 127N 2 Stage IIB 2.5
54
+ X09BR007 X09BR007 Breast Cancer Invasive Breast Carcinoma 7 LumB-I 0.423 BRCA LumA 130N 4 Stage IIIA 1.7
55
+ X11BR003 X11BR003 Breast Cancer Invasive Breast Carcinoma 5 Basal-I 0.784 BRCA Basal 130C 3 Stage IIA 26.7666666667
56
+ X11BR004 X11BR004 Breast Cancer Invasive Breast Carcinoma 5 HER2-I 0.782 BRCA Her2 128C 9 Stage IIA 1.3
57
+ X11BR006 X11BR006 Breast Cancer Invasive Breast Carcinoma 6 LumA-I 0.383 BRCA LumA 127N 8 Stage IIA 2.63333333333
58
+ X11BR009 X11BR009 Breast Cancer Invasive Breast Carcinoma 1 LumB-I 0.776 BRCA LumB 128C 4 Stage IIIC 4.36666666667
59
+ X11BR010 X11BR010 Breast Cancer Invasive Breast Carcinoma 10 HER2-I 0.811 BRCA LumA 129C 6 Stage IIB 1.5
60
+ X11BR011 X11BR011 Breast Cancer Invasive Breast Carcinoma 10 HER2-I 0.648 BRCA LumB 130C|127N 6|17 Stage IIIA 1.46666666667
61
+ X11BR012 X11BR012 Breast Cancer Invasive Breast Carcinoma 9 LumB-I 0.814 BRCA LumA 130N 13 Stage IIA 3.23333333333
62
+ X11BR013 X11BR013 Breast Cancer Invasive Breast Carcinoma 9 LumB-I 0.872 BRCA LumB 129N 5 Stage IIA 2.06666666667
63
+ X11BR014 X11BR014 Breast Cancer Invasive Breast Carcinoma 11 LumA-I 0.72 BRCA LumA 128C 6 Stage IIIA 2.5
64
+ X11BR015 X11BR015 Breast Cancer Invasive Breast Carcinoma 12 LumB-I 0.941 BRCA LumB 127C 9 Stage IIIA 0.933333333333
65
+ X11BR016 X11BR016 Breast Cancer Invasive Breast Carcinoma 12 Basal-I 0.937 BRCA Basal 128C 8 Stage IIA 2.6
66
+ X11BR017 X11BR017 Breast Cancer Invasive Breast Carcinoma 11 HER2-I 0.75 BRCA Her2 127C 2 Stage IIIA 1.66666666667
67
+ X11BR018 X11BR018 Breast Cancer Invasive Breast Carcinoma 11 LumA-I 0.962 BRCA LumA 130C 8 Stage IIIA 2.23333333333
68
+ X11BR019 X11BR019 Breast Cancer Invasive Breast Carcinoma 12 LumB-I 0.658 BRCA LumB 127N 5 Stage IIA 2.96666666667
69
+ X11BR020 X11BR020 Breast Cancer Invasive Breast Carcinoma 10 HER2-I 0.637 BRCA LumA 130C 4 Stage IIA 4.03333333333
70
+ X11BR022 X11BR022 Breast Cancer Invasive Breast Carcinoma 7 LumA-I 0.414 BRCA LumA 128C 5 Stage IIA 1.63333333333
71
+ X11BR023 X11BR023 Breast Cancer Invasive Breast Carcinoma 6 Basal-I 0.957 BRCA Basal 128N 1 Stage IIA 3.56666666667
72
+ X11BR024 X11BR024 Breast Cancer Invasive Breast Carcinoma 7 Basal-I 0.903 BRCA Basal 127C 7 Stage IIA 2.73333333333
73
+ X11BR025 X11BR025 Breast Cancer Invasive Breast Carcinoma 8 LumB-I 0.934 BRCA LumA 128C 2 Stage IIA 1.5
74
+ X11BR027 X11BR027 Breast Cancer Invasive Breast Carcinoma 11 LumB-I 0.738 BRCA LumA 126 11 Stage IIA 3.76666666667
75
+ X11BR028 X11BR028 Breast Cancer Invasive Breast Carcinoma 10 HER2-I 0.588 BRCA Her2 126 4 Stage IIA 3.06666666667
76
+ X11BR030 X11BR030 Breast Cancer Invasive Breast Carcinoma 15 HER2-I 0.78 BRCA Her2 126 6 Stage IIA 2.93333333333
77
+ X11BR031 X11BR031 Breast Cancer Invasive Breast Carcinoma 10 HER2-I 0.572 BRCA LumA 129C|130C 2|5 Stage IIA 11.6333333333
78
+ X11BR032 X11BR032 Breast Cancer Invasive Breast Carcinoma 15 LumA-I 0.632 BRCA LumA 129N 3 Stage IIA 0.6
79
+ X11BR036 X11BR036 Breast Cancer Invasive Breast Carcinoma 15 Basal-I 0.606 BRCA Basal 128C|129C|130N 10|12|17 Stage IIA 2.06666666667
80
+ X11BR038 X11BR038 Breast Cancer Invasive Breast Carcinoma 10 HER2-I 0.726 BRCA Her2 128N 10 Stage IIA 1.4
81
+ X11BR040 X11BR040 Breast Cancer Invasive Breast Carcinoma 5 LumA-I 0.606 BRCA LumA 128N 9 Stage IIIA 1.0
82
+ X11BR042 X11BR042 Breast Cancer Invasive Breast Carcinoma 8 HER2-I 0.978 BRCA Her2 130N 8 Stage IIA 0.9
83
+ X11BR043 X11BR043 Breast Cancer Invasive Breast Carcinoma 8 LumB-I 0.638 BRCA LumB 127N 1 Stage IIB 2.63333333333
84
+ X11BR044 X11BR044 Breast Cancer Invasive Breast Carcinoma 10 LumB-I 0.606 BRCA LumB 128N 8 Stage IIIA 1.6
85
+ X11BR047 X11BR047 Breast Cancer Invasive Breast Carcinoma 15 LumA-I 0.485 BRCA LumA 126 1 Stage IIA 0.833333333333
86
+ X11BR049 X11BR049 Breast Cancer Invasive Breast Carcinoma 10 LumB-I 0.638 BRCA LumB 127C 1 Stage IIIA 2.43333333333
87
+ X11BR050 X11BR050 Breast Cancer Invasive Breast Carcinoma 10 LumA-I 0.862 BRCA LumA 127C 6 Stage IIA 0.9
88
+ X11BR051 X11BR051 Breast Cancer Invasive Breast Carcinoma 10 LumB-I 0.418 BRCA LumA 128N 11 Stage IIIA 1.2
89
+ X11BR053 X11BR053 Breast Cancer Invasive Breast Carcinoma 10 LumB-I 0.744 BRCA LumB 126|129N 3|11 Stage IIA 2.53333333333
90
+ X11BR054 X11BR054 Breast Cancer Invasive Breast Carcinoma 9 LumB-I 0.809 BRCA LumA 130N 7 Stage IIA 0.7
91
+ X11BR055 X11BR055 Breast Cancer Invasive Breast Carcinoma 8 LumA-I 0.641 BRCA LumA 129N 8 Stage IIA 2.53333333333
92
+ X11BR056 X11BR056 Breast Cancer Invasive Breast Carcinoma 15 HER2-I 0.623 BRCA LumA 127C 10 Stage IIB 1.23333333333
93
+ X11BR058 X11BR058 Breast Cancer Invasive Breast Carcinoma 5 HER2-I 0.91 BRCA Normal-like 129C 13 Stage IIA 1.93333333333
94
+ X11BR059 X11BR059 Breast Cancer Invasive Breast Carcinoma 5 HER2-I 0.79 BRCA Normal-like 127C 11 Stage IIA 2.23333333333
95
+ X11BR060 X11BR060 Breast Cancer Invasive Breast Carcinoma 5 HER2-I 0.795 BRCA Her2 129C|126 11|16 Stage IIB 3.66666666667
96
+ X11BR072 X11BR072 Breast Cancer Invasive Breast Carcinoma 5 LumA-I 0.863 BRCA LumA 130C 10 Stage IIIC 1.36666666667
97
+ X11BR073 X11BR073 Breast Cancer Invasive Breast Carcinoma 5 LumB-I 0.472 BRCA LumB 128N 4 Stage IIIA 2.53333333333
98
+ X11BR074 X11BR074 Breast Cancer Invasive Breast Carcinoma 5 LumA-I 0.862 BRCA LumA 129C 1 Stage IIIA 0.633333333333
99
+ X11BR075 X11BR075 Breast Cancer Invasive Breast Carcinoma 5 LumB-I 0.484 BRCA LumB 130C 11 Stage IIIA 5.2
100
+ X11BR080 X11BR080 Breast Cancer Invasive Breast Carcinoma 5 Basal-I 0.767 BRCA Basal 127N 13 Stage IIB 2.23333333333
101
+ X13BR009 X13BR009 Breast Cancer Invasive Breast Carcinoma 22 LumB-I 0.618 BRCA LumB 126 13 Stage IIIB 1.96666666667
102
+ X14BR005 X14BR005 Breast Cancer Invasive Breast Carcinoma 12 LumB-I 0.871 BRCA LumA 127C|130C 8|16 Stage IIA 1.03333333333
103
+ X14BR008 X14BR008 Breast Cancer Invasive Breast Carcinoma 22 LumA-I 0.988 BRCA LumA 127C 3 Stage IIIA 0.766666666667
104
+ X14BR014 X14BR014 Breast Cancer Invasive Breast Carcinoma 18 LumA-I 0.828 BRCA LumA 129N 13 Stage IIA 0.7
105
+ X15BR003 X15BR003 Breast Cancer Invasive Breast Carcinoma 1 LumA-I 0.849 BRCA LumA 128C 13 Stage IIA 22.0
106
+ X16BR012 X16BR012 Breast Cancer Invasive Breast Carcinoma 20 LumB-I 0.43 BRCA LumB 127C 12 Stage IIIC 5.46666666667
107
+ X18BR002 X18BR002 Breast Cancer Invasive Breast Carcinoma 11 HER2-I 0.533 BRCA Her2 128N 3 Stage IIIA 4.93333333333
108
+ X18BR003 X18BR003 Breast Cancer Invasive Breast Carcinoma 7 LumB-I 0.612 BRCA LumB 127N 7 Stage IIA 33.5666666667
109
+ X18BR004 X18BR004 Breast Cancer Invasive Breast Carcinoma 8 LumB-I 0.837 BRCA LumA 127N 4 Stage IIA 0.933333333333
110
+ X18BR006 X18BR006 Breast Cancer Invasive Breast Carcinoma 8 LumB-I 0.371 BRCA LumB 129C 10 Stage IIA 4.23333333333
111
+ X18BR007 X18BR007 Breast Cancer Invasive Breast Carcinoma 11 LumA-I 0.615 BRCA LumA 127N 6 Stage IIA 3.2
112
+ X18BR009 X18BR009 Breast Cancer Invasive Breast Carcinoma 7 HER2-I 0.578 BRCA Normal-like 129N 10 Stage IIA 2.03333333333
113
+ X18BR010 X18BR010 Breast Cancer Invasive Breast Carcinoma 5 LumA-I 0.69 BRCA LumA 128C 1 Stage IIIA 0.8
114
+ X18BR016 X18BR016 Breast Cancer Invasive Breast Carcinoma 9 LumA-I 0.757 BRCA LumA 130N 12 Stage IA 1.16666666667
115
+ X18BR017 X18BR017 Breast Cancer Invasive Breast Carcinoma 14 HER2-I 0.539 BRCA LumA 130N 1 Stage IA 2.56666666667
116
+ X18BR019 X18BR019 Breast Cancer Invasive Breast Carcinoma 13 LumB-I 0.569 BRCA LumA 129N 4 Stage IIIA 1.0
117
+ X20BR001 X20BR001 Breast Cancer Invasive Breast Carcinoma 22 LumB-I 0.711 BRCA LumA 129C 4 Stage IIA 1.1
118
+ X20BR002 X20BR002 Breast Cancer Invasive Breast Carcinoma 16 Basal-I 0.711 BRCA Basal 126 5 Stage IIA 3.53333333333
119
+ X20BR005 X20BR005 Breast Cancer Invasive Breast Carcinoma 26 Basal-I 0.632 BRCA Basal 127C 4 Stage IIB 4.16666666667
120
+ X20BR006 X20BR006 Breast Cancer Invasive Breast Carcinoma 18 Basal-I 0.728 BRCA Basal 128N 17 Stage IIB 2.9
121
+ X20BR007 X20BR007 Breast Cancer Invasive Breast Carcinoma 16 Basal-I 0.609 BRCA Basal 130N 5 Stage IIA 4.06666666667
122
+ X20BR008 X20BR008 Breast Cancer Invasive Breast Carcinoma 11 HER2-I 0.481 BRCA Her2 127C 5 Stage IIIB 2.83333333333
123
+ X21BR001 X21BR001 Breast Cancer Invasive Breast Carcinoma NA LumB-I 0.536 BRCA LumB 128N 16 NA 8.73333333333
124
+ X21BR002 X21BR002 Breast Cancer Invasive Breast Carcinoma NA LumB-I 0.443 BRCA LumA 128C 16 NA 1.6
125
+ X21BR010 X21BR010 Breast Cancer Invasive Breast Carcinoma 18 LumA-I 0.559 BRCA LumA 129C|128C 3|17 Stage IIA 0.8
126
+ X22BR005 X22BR005 Breast Cancer Invasive Breast Carcinoma 20 LumB-I 0.392 BRCA LumA 129N 6 Stage IIB 2.93333333333
127
+ X22BR006 X22BR006 Breast Cancer Invasive Breast Carcinoma 25 LumB-I 0.402 BRCA LumA 130N 10 Stage IIIA 0.666666666667
data/cBioPortal/brca_cptac_2020/data_cna.txt ADDED
The diff for this file is too large to render. See raw diff
 
data/cBioPortal/brca_cptac_2020/data_gene_panel_matrix.txt ADDED
@@ -0,0 +1,123 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ SAMPLE_ID mutations gistic
2
+ CPT000814 WXS WXS
3
+ CPT001846 WXS WXS
4
+ X01BR001 WXS WXS
5
+ X01BR008 WXS WXS
6
+ X01BR009 WXS WXS
7
+ X01BR010 WXS WXS
8
+ X01BR015 WXS WXS
9
+ X01BR017 WXS WXS
10
+ X01BR018 WXS WXS
11
+ X01BR020 WXS WXS
12
+ X01BR023 WXS WXS
13
+ X01BR025 WXS WXS
14
+ X01BR026 WXS WXS
15
+ X01BR027 WXS WXS
16
+ X01BR030 WXS WXS
17
+ X01BR031 WXS WXS
18
+ X01BR032 WXS WXS
19
+ X01BR033 WXS WXS
20
+ X01BR040 WXS WXS
21
+ X01BR042 WXS WXS
22
+ X01BR043 WXS WXS
23
+ X03BR002 WXS WXS
24
+ X03BR004 WXS WXS
25
+ X03BR005 WXS WXS
26
+ X03BR006 WXS WXS
27
+ X03BR010 WXS WXS
28
+ X03BR011 WXS WXS
29
+ X03BR013 WXS WXS
30
+ X05BR001 WXS WXS
31
+ X05BR003 WXS WXS
32
+ X05BR004 WXS WXS
33
+ X05BR005 WXS WXS
34
+ X05BR009 WXS WXS
35
+ X05BR016 WXS WXS
36
+ X05BR026 WXS WXS
37
+ X05BR029 WXS WXS
38
+ X05BR038 WXS WXS
39
+ X05BR042 WXS WXS
40
+ X05BR043 WXS WXS
41
+ X05BR044 WXS WXS
42
+ X05BR045 WXS WXS
43
+ X06BR003 WXS WXS
44
+ X06BR005 WXS WXS
45
+ X06BR006 WXS WXS
46
+ X06BR014 WXS WXS
47
+ X09BR001 WXS WXS
48
+ X09BR004 WXS WXS
49
+ X09BR005 WXS WXS
50
+ X09BR007 WXS WXS
51
+ X11BR003 WXS WXS
52
+ X11BR004 WXS WXS
53
+ X11BR006 WXS WXS
54
+ X11BR009 WXS WXS
55
+ X11BR010 WXS WXS
56
+ X11BR011 WXS WXS
57
+ X11BR012 WXS WXS
58
+ X11BR013 WXS WXS
59
+ X11BR014 WXS WXS
60
+ X11BR015 WXS WXS
61
+ X11BR016 WXS WXS
62
+ X11BR017 WXS WXS
63
+ X11BR018 WXS WXS
64
+ X11BR019 WXS WXS
65
+ X11BR020 WXS WXS
66
+ X11BR022 WXS WXS
67
+ X11BR023 WXS WXS
68
+ X11BR024 WXS WXS
69
+ X11BR025 WXS WXS
70
+ X11BR027 WXS WXS
71
+ X11BR028 WXS WXS
72
+ X11BR030 WXS WXS
73
+ X11BR031 WXS WXS
74
+ X11BR032 WXS WXS
75
+ X11BR036 WXS WXS
76
+ X11BR038 WXS WXS
77
+ X11BR040 WXS WXS
78
+ X11BR042 WXS WXS
79
+ X11BR043 WXS WXS
80
+ X11BR044 WXS WXS
81
+ X11BR047 WXS WXS
82
+ X11BR049 WXS WXS
83
+ X11BR050 WXS WXS
84
+ X11BR051 WXS WXS
85
+ X11BR053 WXS WXS
86
+ X11BR054 WXS WXS
87
+ X11BR055 WXS WXS
88
+ X11BR056 WXS WXS
89
+ X11BR058 WXS WXS
90
+ X11BR059 WXS WXS
91
+ X11BR060 WXS WXS
92
+ X11BR072 WXS WXS
93
+ X11BR073 WXS WXS
94
+ X11BR074 WXS WXS
95
+ X11BR075 WXS WXS
96
+ X11BR080 WXS WXS
97
+ X13BR009 WXS WXS
98
+ X14BR005 WXS WXS
99
+ X14BR008 WXS WXS
100
+ X14BR014 WXS WXS
101
+ X15BR003 WXS WXS
102
+ X16BR012 WXS WXS
103
+ X18BR002 WXS WXS
104
+ X18BR003 WXS WXS
105
+ X18BR004 WXS WXS
106
+ X18BR006 WXS WXS
107
+ X18BR007 WXS WXS
108
+ X18BR009 WXS WXS
109
+ X18BR010 WXS WXS
110
+ X18BR016 WXS WXS
111
+ X18BR017 WXS WXS
112
+ X18BR019 WXS WXS
113
+ X20BR001 WXS WXS
114
+ X20BR002 WXS WXS
115
+ X20BR005 WXS WXS
116
+ X20BR006 WXS WXS
117
+ X20BR007 WXS WXS
118
+ X20BR008 WXS WXS
119
+ X21BR001 WXS WXS
120
+ X21BR002 WXS WXS
121
+ X21BR010 WXS WXS
122
+ X22BR005 WXS WXS
123
+ X22BR006 WXS WXS
data/cBioPortal/brca_cptac_2020/data_log2_cna.txt ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:365a93a096b4ccfd099117629bf78eefbfa96aca9a52d6d1572b4fa75fee23d9
3
+ size 18527689
data/cBioPortal/brca_cptac_2020/data_mrna_seq_fpkm.txt ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:00614131229ee33188d7dd20be12d2ac297c052840d93480681852f44e9d0b19
3
+ size 17773792
data/cBioPortal/brca_cptac_2020/data_mrna_seq_fpkm_zscores_ref_all_samples.txt ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:21d013fd325ce28809b9f4b68411e6b1d16171b4bd122d898f66a0c83c59406d
3
+ size 26218357
data/cBioPortal/brca_cptac_2020/data_mutations.txt ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:f93eedaad8c9165649fc963c5c7291914729968652c73acbf639c92f4e9c9d89
3
+ size 28614677
data/cBioPortal/brca_cptac_2020/data_phosphoprotein_quantification.txt ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:aef2c0d99e94a3b93a5aef12a4d98a300d7fbaa19e84645d6e7e89fa831a533d
3
+ size 31833718
data/cBioPortal/brca_cptac_2020/data_protein_quantification.txt ADDED
The diff for this file is too large to render. See raw diff
 
data/cBioPortal/brca_cptac_2020/data_protein_quantification_zscores_ref_all_samples.txt ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:b22ea822ddc6d8b0c46a436645df572a691661facafa3e69cc11b0baf8ab9fda
3
+ size 12657032
data/cBioPortal/brca_cptac_2020/meta_acetylprotein_quantification.txt ADDED
@@ -0,0 +1,10 @@
 
 
 
 
 
 
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ genetic_alteration_type: GENERIC_ASSAY
3
+ generic_assay_type: Acetylproteome
4
+ datatype: LIMIT-VALUE
5
+ stable_id: acetylproteome
6
+ show_profile_in_analysis_tab: true
7
+ profile_name: Acetylprotein abundance ratio
8
+ profile_description: Abundance ratio for acetylproteins measured by mass spectrometry. Column ACETYLSITES: sites_#sites_#present_firstAA_lastAA
9
+ data_filename: data_acetylprotein_quantification.txt
10
+ generic_entity_meta_properties: NAME,DESCRIPTION,GENE_SYMBOL,ACETYLSITES
data/cBioPortal/brca_cptac_2020/meta_clinical_patient.txt ADDED
@@ -0,0 +1,4 @@
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ genetic_alteration_type: CLINICAL
3
+ datatype: PATIENT_ATTRIBUTES
4
+ data_filename: data_clinical_patient.txt
data/cBioPortal/brca_cptac_2020/meta_clinical_sample.txt ADDED
@@ -0,0 +1,4 @@
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ genetic_alteration_type: CLINICAL
3
+ datatype: SAMPLE_ATTRIBUTES
4
+ data_filename: data_clinical_sample.txt
data/cBioPortal/brca_cptac_2020/meta_cna.txt ADDED
@@ -0,0 +1,8 @@
 
 
 
 
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ genetic_alteration_type: COPY_NUMBER_ALTERATION
3
+ datatype: DISCRETE
4
+ stable_id: gistic
5
+ show_profile_in_analysis_tab: true
6
+ profile_name: Discrete copy number alteration values
7
+ profile_description: Discrete copy number alterations based on continuous data
8
+ data_filename: data_cna.txt
data/cBioPortal/brca_cptac_2020/meta_gene_panel_matrix.txt ADDED
@@ -0,0 +1,4 @@
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ genetic_alteration_type: GENE_PANEL_MATRIX
3
+ datatype: GENE_PANEL_MATRIX
4
+ data_filename: data_gene_panel_matrix.txt
data/cBioPortal/brca_cptac_2020/meta_log2_cna.txt ADDED
@@ -0,0 +1,8 @@
 
 
 
 
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ genetic_alteration_type: COPY_NUMBER_ALTERATION
3
+ datatype: LOG2-VALUE
4
+ stable_id: log2CNA
5
+ show_profile_in_analysis_tab: false
6
+ profile_name: Copy number alteration values
7
+ profile_description: Copy number alteration values by Gistic 2
8
+ data_filename: data_log2_cna.txt
data/cBioPortal/brca_cptac_2020/meta_mrna_seq_fpkm.txt ADDED
@@ -0,0 +1,8 @@
 
 
 
 
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ genetic_alteration_type: MRNA_EXPRESSION
3
+ datatype: CONTINUOUS
4
+ stable_id: rna_seq_v2_mrna
5
+ show_profile_in_analysis_tab: false
6
+ profile_name: mRNA expression (FPKM, log2 transformed)
7
+ profile_description: Gene expression by mRNA abundance in FPKM values (values of 0 were considered as missing and replaced by NA before applying log2 transformation)
8
+ data_filename: data_mrna_seq_fpkm.txt
data/cBioPortal/brca_cptac_2020/meta_mrna_seq_fpkm_zscores_ref_all_samples.txt ADDED
@@ -0,0 +1,8 @@
 
 
 
 
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ genetic_alteration_type: MRNA_EXPRESSION
3
+ datatype: Z-SCORE
4
+ stable_id: mrna_median_Zscores
5
+ show_profile_in_analysis_tab: true
6
+ profile_name: Z-scores of mRNA expression (FPKM, log2 transformed)
7
+ profile_description: Z-scores of mRNA abundance in FPKM values (log2 transformed), calculated over all patients
8
+ data_filename: data_mrna_seq_fpkm_zscores_ref_all_samples.txt
data/cBioPortal/brca_cptac_2020/meta_mutations.txt ADDED
@@ -0,0 +1,8 @@
 
 
 
 
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ genetic_alteration_type: MUTATION_EXTENDED
3
+ datatype: MAF
4
+ stable_id: mutations
5
+ show_profile_in_analysis_tab: true
6
+ profile_name: Mutations
7
+ profile_description: Mutations
8
+ data_filename: data_mutations.txt
data/cBioPortal/brca_cptac_2020/meta_phosphoprotein_quantification.txt ADDED
@@ -0,0 +1,10 @@
 
 
 
 
 
 
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ genetic_alteration_type: GENERIC_ASSAY
3
+ generic_assay_type: Phosphoproteome
4
+ datatype: LIMIT-VALUE
5
+ stable_id: phosphoproteome
6
+ show_profile_in_analysis_tab: true
7
+ profile_name: Phosphoprotein abundance ratio
8
+ profile_description: Abundance ratio for phosphoproteins measured by mass spectrometry. Column PHOSPHOSITES: sites_#sites_#present_firstAA_lastAA
9
+ data_filename: data_phosphoprotein_quantification.txt
10
+ generic_entity_meta_properties: NAME,DESCRIPTION,GENE_SYMBOL,PHOSPHOSITES
data/cBioPortal/brca_cptac_2020/meta_protein_quantification.txt ADDED
@@ -0,0 +1,8 @@
 
 
 
 
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ genetic_alteration_type: PROTEIN_LEVEL
3
+ datatype: LOG2-VALUE
4
+ stable_id: protein_quantification
5
+ show_profile_in_analysis_tab: false
6
+ profile_name: Protein abundance ratio
7
+ profile_description: Protein abundance ratio measured by mass spectrometry
8
+ data_filename: data_protein_quantification.txt
data/cBioPortal/brca_cptac_2020/meta_protein_quantification_zscores_ref_all_samples.txt ADDED
@@ -0,0 +1,8 @@
 
 
 
 
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ genetic_alteration_type: PROTEIN_LEVEL
3
+ datatype: Z-SCORE
4
+ stable_id: protein_quantification_zscores
5
+ show_profile_in_analysis_tab: true
6
+ profile_name: Protein abundance ratio Z-scores
7
+ profile_description: Z-scores of protein abundance ratio measured by mass spectrometry
8
+ data_filename: data_protein_quantification_zscores_ref_all_samples.txt
data/cBioPortal/brca_cptac_2020/meta_study.txt ADDED
@@ -0,0 +1,9 @@
 
 
 
 
 
 
 
 
 
 
1
+ cancer_study_identifier: brca_cptac_2020
2
+ name: Proteogenomic landscape of breast cancer (CPTAC, Cell 2020)
3
+ short_name: Breast Cancer (CPTAC, Cell 2020)
4
+ description: Proteogenomic landscape of breast cancer tumorigenesis and targeted therapy. Whole exome sequencing 122 samples. Generated by CPTAC.
5
+ groups: PUBLIC
6
+ pmid: 33212010
7
+ citation: Krug et al. Cell 2020
8
+ type_of_cancer: brca
9
+ groups: PUBLIC