Pan-cancer Aberrant Pathway Activity Analysis (PAPAA)

<p>Information about the dataset files:</p> <p>1) pancan_rnaseq_freeze.tsv.gz: Publicly available gene expression data for the TCGA Pan-cancer dataset. File: PanCanAtlas&nbsp;EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv was processed using script process_sample_freeze.py by&nbsp;Gregory Way et al as described in&nbsp;https://github.com/greenelab/pancancer/ data processing and initialization&nbsp;steps. [http://api.gdc.cancer.gov/data/3586c0da-64d0-4b74-a449-5ff4d9136611] [<a href="https://doi.org/10.1016/j.celrep.2018.03.046">https://doi.org/10.1016/j.celrep.2018.03.046</a>]</p> <p>2)&nbsp;pancan_mutation_freeze.tsv.gz:&nbsp;Publicly available Mutational information for&nbsp;TCGA Pan-cancer dataset.&nbsp; File: mc3.v0.2.8.PUBLIC.maf.gz&nbsp;was processed using script process_sample_freeze.py by Gregory Way et al as described in https://github.com/greenelab/pancancer/ data processing and initialization steps. [http://api.gdc.cancer.gov/data/1c8cfe5f-e52d-41ba-94da-f15ea1337efc]&nbsp;[https://doi.org/10.1016/j.celrep.2018.03.046]&nbsp;</p> <p>3) pancan_GISTIC_threshold.tsv.gz:&nbsp;Publicly available Gene- level copy number information of the TCGA Pan-cancer dataset. This file is processed using script process_copynumber.py&nbsp;&nbsp;by&nbsp;Gregory Way et al&nbsp;as described in https://github.com/greenelab/pancancer/ data processing and initialization steps. The files&nbsp;copy_number_loss_status.tsv.gz and&nbsp;copy_number_gain_status.tsv.gz generated from this data are used as inputs in our Galaxy pipeline.&nbsp;[https://xenabrowser.net/datapages/?cohort=TCGA%20Pan-Cancer%20(PANCAN)&amp;removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443] [<a href="https://doi.org/10.1016/j.celrep.2018.03.046">https://doi.org/10.1016/j.celrep.2018.03.046</a>]</p> <p>4)&nbsp;mutation_burden_freeze.tsv.gz:&nbsp;Publicly available Mutational information for&nbsp;TCGA Pan-cancer dataset&nbsp; mc3.v0.2.8.PUBLIC.maf.gz&nbsp;was processed using script process_sample_freeze.py by Gregory Way et al as described in https://github.com/greenelab/pancancer/ data processing and initialization steps. [https://github.com/greenelab/pancancer/][http://api.gdc.cancer.gov/data/1c8cfe5f-e52d-41ba-94da-f15ea1337efc]&nbsp;[https://doi.org/10.1016/j.celrep.2018.03.046]</p> <p>5) sample_freeze.tsv or sample_freeze_version4_modify.tsv: The file lists the frozen samples as determined by&nbsp;TCGA PanCancer Atlas consortium along with raw RNAseq and mutation data. These were previously determined and included for all downstream analysis All other datasets were processed and subset according to the frozen samples.[https://github.com/greenelab/pancancer/]</p> <p>6)&nbsp;cosmic_cancer_classification.tsv: Compendium&nbsp;of&nbsp;OG and TSG used for the analysis. Added additional genes from the cosmic database to volgelstein_cancer_classification.tsv&nbsp;[https://github.com/greenelab/pancancer/]</p> <p>7)&nbsp;CCLE_DepMap_18Q1_maf_20180207.txt.gz Publicly available Mutational data for CCLE cell lines from Broad Institute Cancer Cell Line Encyclopedia (CCLE) / DepMap Portal. [https://depmap.org/portal/download/api/download/external?file_name=ccle%2FCCLE_DepMap_18Q1_maf_20180207.txt]</p> <p>8)&nbsp;ccle_rnaseq_genes_rpkm_20180929_mod.tsv.gz: Publicly available Expression data for 1019 cell lines (RPKM) from&nbsp;&nbsp;Broad Institute Cancer Cell Line Encyclopedia (CCLE) / DepMap Portal. [https://depmap.org/portal/download/api/download/external?file_name=ccle%2Fccle_2019%2FCCLE_RNAseq_genes_rpkm_20180929.gct.gz]</p> <p>9)&nbsp;CCLE_MUT_CNA_AMP_DEL_binary_Revealer.tsv:&nbsp;Publicly available merged Mutational and copy number alterations that include gene amplifications and deletions for the CCLE cell lines. This&nbsp;data is represented in the binary format and provided by the Broad&nbsp;Institute Cancer Cell Line Encyclopedia (CCLE) / DepMap Portal. [https://data.broadinstitute.org/ccle_legacy_data/binary_calls_for_copy_number_and_mutation_data/CCLE_MUT_CNA_AMP_DEL_binary_Revealer.gct]</p> <p>10)&nbsp;GDSC_cell_lines_EXP_CCLE_names.tsv.gz Publicly available RMA normalized expression data for Genomics of Drug Sensitivity in Cancer(GDSC)&nbsp;cell-lines. File&nbsp;gdsc_cell_line_RMA_proc_basalExp.csv was downloaded. This data was subsetted to 389 cell lines that are common among CCLE and GDSC. All the GDSC cell line&nbsp;names were replaced with CCLE cell line names for further processing. [https://www.cancerrxgene.org/gdsc1000/GDSC1000_WebResources//Data/preprocessed/Cell_line_RMA_proc_basalExp.txt.zip]</p> <p>11)&nbsp;GDSC_CCLE_common_mut_cnv_binary.tsv.gz:&nbsp;&nbsp;&nbsp;A subset of&nbsp;merged Mutational and copy number alterations that include gene amplifications and deletions for common cell lines between GDSC and CCLE. This file is generated using CCLE_MUT_CNA_AMP_DEL_binary_Revealer.tsv&nbsp;and a list of common cell lines.&nbsp;</p> <p>12)&nbsp;gdsc1_ccle_pharm_fitted_dose_data.txt.gz: Pharmacological data for GDSC1 cell lines. [ftp://ftp.sanger.ac.uk/pub/project/cancerrxgene/releases/current_release/GDSC1_fitted_dose_response_15Oct19.xlsx]</p> <p>13)&nbsp;gdsc2_ccle_pharm_fitted_dose_data.txt.gz: Pharmacological data for GDSC2&nbsp;cell lines. [ftp://ftp.sanger.ac.uk/pub/project/cancerrxgene/releases/current_release/GDSC2_fitted_dose_response_15Oct19.xlsx]</p> <p>14) compounds_of_interest.txt: list of pharmacological compounds tested for our analysis,&nbsp; taken from ftp://ftp.sanger.ac.uk/pub4/cancerrxgene/releases/release-8.1/screened_compounds_rel_8.1.csv.&nbsp;&nbsp;</p> <p>15) tcga_dictonary.tsv: list of cancer types used in the analysis.&nbsp;</p> <p>16) seg_based_scores.tsv: Measurement of total copy number burden,&nbsp;Percent of genome altered by copy number alterations. This file was used as part of the Pancancer analysis by Gregory Way et al as described in https://github.com/greenelab/pancancer/ data processing and initialization steps. [https://github.com/greenelab/pancancer/]</p> <p>17) GSE69822_pi3k_sign.txt: File with&nbsp;values&nbsp;assigned for tumor [1] or normal [-1]&nbsp; in given external samples (GSE69822)</p> <p>18) vlog_trans.csv: Variant stabilized log-transformed expression&nbsp;values in given external samples (GSE69822)</p> <p>19) path_rtk_ras_pi3k_genes.txt: File with the list of ERK/RAS/PI3K pathway genes used in the analysis.&nbsp;</p> <p>20)&nbsp;path_myc_genes.txt:&nbsp;File with the list of Myc&nbsp;pathway genes used in the analysis. (Sanchez-Vega, Francisco et al.)</p> <p>21)&nbsp;&nbsp;path_ras_genes.txt:&nbsp;File with the list of RAS&nbsp;pathway genes used in the analysis. (Sanchez-Vega, Francisco et al.)</p> <p>22)&nbsp;path_cell_cycle_genes.txt:&nbsp;File with the list of cell cycle pathway genes used in the analysis. (Sanchez-Vega, Francisco et al.)</p> <p>23)&nbsp;&nbsp;path_wnt_genes.txt:&nbsp;File with the list of WNT pathway genes used in the analysis. (Sanchez-Vega, Francisco et al.)</p> <p>24) GSE94937_rpkm_kras.csv: Expression&nbsp;values in given external samples (GSE94937)</p> <p>25) GSE94937_kras_sign.txt:&nbsp;File with&nbsp;values&nbsp;assigned for KRAS Mutant&nbsp;[1] or WT [-1]&nbsp; in given external samples (GSE94937)</p>