Pan-cancer Aberrant Pathway Activity Analysis (PAPAA)

Information about the dataset files: 1) pancan_rnaseq_freeze.tsv.gz: Publicly available gene expression data for the TCGA Pan-cancer dataset. File: PanCanAtlas EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv 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/3586c0da-64d0-4b74-a449-5ff4d9136611] [https://doi.org/10.1016/j.celrep.2018.03.046] 2) pancan_mutation_freeze.tsv.gz: Publicly available Mutational information for TCGA Pan-cancer dataset. File: mc3.v0.2.8.PUBLIC.maf.gz 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] [https://doi.org/10.1016/j.celrep.2018.03.046] 3) pancan_GISTIC_threshold.tsv.gz: Publicly available Gene- level copy number information of the TCGA Pan-cancer dataset. This file is processed using script process_copynumber.py by Gregory Way et al as described in https://github.com/greenelab/pancancer/ data processing and initialization steps. The files copy_number_loss_status.tsv.gz and copy_number_gain_status.tsv.gz generated from this data are used as inputs in our Galaxy pipeline. [https://xenabrowser.net/datapages/?cohort=TCGA%20Pan-Cancer%20(PANCAN)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443] [https://doi.org/10.1016/j.celrep.2018.03.046] 4) mutation_burden_freeze.tsv.gz: Publicly available Mutational information for TCGA Pan-cancer dataset mc3.v0.2.8.PUBLIC.maf.gz 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] [https://doi.org/10.1016/j.celrep.2018.03.046] 5) sample_freeze.tsv or sample_freeze_version4_modify.tsv: The file lists the frozen samples as determined by 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/] 6) vogelstein_cancergenes.tsv: compendium of OG and TSG used for the analysis. [https://github.com/greenelab/pancancer/] 7) 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] 8) ccle_rnaseq_genes_rpkm_20180929.gct.gz: Publicly available Expression data for 1019 cell lines (RPKM) from 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] 9) CCLE_MUT_CNA_AMP_DEL_binary_Revealer.gct: Publicly available merged Mutational and copy number alterations that include gene amplifications and deletions for the CCLE cell lines. This data is represented in the binary format and provided by the Broad 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] 10) GDSC_cell_lines_EXP_CCLE_names.csv.gz Publicly available RMA normalized expression data for Genomics of Drug Sensitivity in Cancer(GDSC) cell-lines. File 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 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] 11) GDSC_CCLE_common_mut_cnv_binary.csv.gz: A subset of 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.gct and a list of common cell lines. 12) 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] 13) gdsc2_ccle_pharm_fitted_dose_data.txt.gz: Pharmacological data for GDSC2 cell lines. [ftp://ftp.sanger.ac.uk/pub/project/cancerrxgene/releases/current_release/GDSC2_fitted_dose_response_15Oct19.xlsx] 14) compounds.csv: list of pharmacological compounds tested for our analysis 15) tcga_dictonary.tsv: list of cancer types used in the analysis. 16) seg_based_scores.tsv: Measurement of total copy number burden, 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/] 17) sign.csv: file with original values assigned for tumor [1] or normal [-1] for given external samples (GSE69822) 18) vlog_trans.csv: variant stabilized log transformed expression values for given external samples (GSE69822) 19 path_genes.csv: file with list of ERK/RAS/PI3K pathway genes used in the analysis.本数据集包含以下文件的相关说明：1) pancan_rnaseq_freeze.tsv.gz：公开获取的TCGA泛癌数据集（TCGA Pan-cancer dataset）基因表达数据。原始文件为PanCanAtlas EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv，由Gregory Way等人基于脚本process_sample_freeze.py，按照https://github.com/greenelab/pancancer/ 中记载的数据处理与初始化流程进行处理。数据来源链接：[http://api.gdc.cancer.gov/data/3586c0da-64d0-4b74-a449-5ff4d9136611]，文献DOI：[https://doi.org/10.1016/j.celrep.2018.03.046] 2) pancan_mutation_freeze.tsv.gz：公开获取的TCGA泛癌数据集突变信息。原始文件为mc3.v0.2.8.PUBLIC.maf.gz，由Gregory Way等人基于脚本process_sample_freeze.py，按照https://github.com/greenelab/pancancer/ 中记载的数据处理与初始化流程进行处理。数据来源链接：[http://api.gdc.cancer.gov/data/1c8cfe5f-e52d-41ba-94da-f15ea1337efc]，文献DOI：[https://doi.org/10.1016/j.celrep.2018.03.046] 3) pancan_GISTIC_threshold.tsv.gz：公开获取的TCGA泛癌数据集基因水平拷贝数信息。该文件由Gregory Way等人基于脚本process_copynumber.py，按照https://github.com/greenelab/pancancer/ 中记载的数据处理与初始化流程进行处理。由此数据生成的copy_number_loss_status.tsv.gz与copy_number_gain_status.tsv.gz文件将作为输入用于本研究的Galaxy分析流程。数据来源链接：[https://xenabrowser.net/datapages/?cohort=TCGA%20Pan-Cancer%20(PANCAN)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443]，文献DOI：[https://doi.org/10.1016/j.celrep.2018.03.046] 4) mutation_burden_freeze.tsv.gz：公开获取的TCGA泛癌数据集突变信息。原始文件mc3.v0.2.8.PUBLIC.maf.gz由Gregory Way等人基于脚本process_sample_freeze.py，按照https://github.com/greenelab/pancancer/ 中记载的数据处理与初始化流程进行处理。数据来源链接：[https://github.com/greenelab/pancancer/][http://api.gdc.cancer.gov/data/1c8cfe5f-e52d-41ba-94da-f15ea1337efc]，文献DOI：[https://doi.org/10.1016/j.celrep.2018.03.046] 5) sample_freeze.tsv 或 sample_freeze_version4_modify.tsv：该文件列出了TCGA泛癌图谱联盟确定的冷冻样本，包含原始RNA测序与突变数据。所有后续分析均采用此前确定的该批样本，其余数据集均按照该批冷冻样本进行处理与子集筛选。数据来源：[https://github.com/greenelab/pancancer/] 6) vogelstein_cancergenes.tsv：本分析所用癌基因（Oncogene, OG）与肿瘤抑制基因（Tumor Suppressor Gene, TSG）汇总表。数据来源：[https://github.com/greenelab/pancancer/] 7) CCLE_DepMap_18Q1_maf_20180207.txt.gz：公开获取的布罗德研究所癌症细胞系百科全书（Cancer Cell Line Encyclopedia, CCLE）/DepMap门户提供的CCLE细胞系突变数据。数据来源链接：[https://depmap.org/portal/download/api/download/external?file_name=ccle%2FCCLE_DepMap_18Q1_maf_20180207.txt] 8) ccle_rnaseq_genes_rpkm_20180929.gct.gz：公开获取的布罗德研究所CCLE/DepMap门户提供的1019株细胞系的RPKM表达数据。数据来源链接：[https://depmap.org/portal/download/api/download/external?file_name=ccle%2Fccle_2019%2FCCLE_RNAseq_genes_rpkm_20180929.gct.gz] 9) CCLE_MUT_CNA_AMP_DEL_binary_Revealer.gct：公开获取的布罗德研究所CCLE/DepMap门户提供的CCLE细胞系合并突变与拷贝数变异数据，包含基因扩增与缺失信息，采用二进制格式表示。数据来源链接：[https://data.broadinstitute.org/ccle_legacy_data/binary_calls_for_copy_number_and_mutation_data/CCLE_MUT_CNA_AMP_DEL_binary_Revealer.gct] 10) GDSC_cell_lines_EXP_CCLE_names.csv.gz：公开获取的癌症药物敏感性基因组学（Genomics of Drug Sensitivity in Cancer, GDSC）细胞系的RMA标准化表达数据。原始下载文件为gdsc_cell_line_RMA_proc_basalExp.csv，本数据集将其筛选为CCLE与GDSC共有的389株细胞系，并将所有GDSC细胞系名称替换为CCLE细胞系名称以用于后续分析。数据来源链接：[https://www.cancerrxgene.org/gdsc1000/GDSC1000_WebResources//Data/preprocessed/Cell_line_RMA_proc_basalExp.txt.zip] 11) GDSC_CCLE_common_mut_cnv_binary.csv.gz：GDSC与CCLE共有细胞系的合并突变与拷贝数变异子集文件，包含基因扩增与缺失信息。该文件基于CCLE_MUT_CNA_AMP_DEL_binary_Revealer.gct与共有细胞系列表生成。 12) gdsc1_ccle_pharm_fitted_dose_data.txt.gz：GDSC1细胞系的药理学数据。数据来源链接：[ftp://ftp.sanger.ac.uk/pub/project/cancerrxgene/releases/current_release/GDSC1_fitted_dose_response_15Oct19.xlsx] 13) gdsc2_ccle_pharm_fitted_dose_data.txt.gz：GDSC2细胞系的药理学数据。数据来源链接：[ftp://ftp.sanger.ac.uk/pub/project/cancerrxgene/releases/current_release/GDSC2_fitted_dose_response_15Oct19.xlsx] 14) compounds.csv：本分析所用受试药理学化合物列表。 15) tcga_dictonary.tsv：本分析所涉癌症类型列表。 16) seg_based_scores.tsv：全基因组拷贝数负担测量文件，即由拷贝数变异所改变的基因组百分比。该文件曾被Gregory Way等人用于泛癌分析，相关处理流程详见https://github.com/greenelab/pancancer/ 中记载的数据处理与初始化步骤。数据来源：[https://github.com/greenelab/pancancer/] 17) sign.csv：针对外部样本GSE69822，为肿瘤样本赋值1、正常样本赋值-1的原始值文件。 18) vlog_trans.csv：针对外部样本GSE69822的变异稳定对数转换表达值文件。 19) path_genes.csv：本分析所用ERK/RAS/PI3K通路基因列表。