SOPA and SIMPA: Normalized single sample integrated multiomics pathway analysis of tumor heterogeneity in solid cancers

This repository contains all raw data obtained from The Cancer Genome Atlas, through the custom search criteria used in the single-omic single-sample pathway anaylsis pipeline (SOPA) and its integrated multiomics extension, SIMPA. .rar files: CNV.rar: Contains copy number variation data. RNAseq.rar: Contains transcriptomics data. Meth.rar: Contains DNA methylation data. SOPA_SIMPA_res.rar: Contains results for SOPA and SIMPA obtained through running the pipeline on the rankings obtained from the custom ranking metrics calculated from the raw data. ssGSEA_GDC_res.rar: Results from running ssGSEA on GDC samples (n = 1,968). GSVA_GDC_res.rar: Results from running GSVA on GDC samples (n = 1,968). Datasets.rar: Contains various results from the analyses made for SOPA/ SIMPA validation and testing. Each of these files was generated from the jupyter notebooks in the linked GitHub repository. The results are as follows: clin.csv: - contains clinical information for the integrated multiomics population p2preinteg_raw_rnaseq_counts.csv: - raw counts for differential expression analysis pre-alignment p2preinteg_tpm_rnaseq_counts.csv: - tpm counts pre-alignment p2preinteg_cnv_counts.csv: - CNVs pre-alignment pre-imputation p2preinteg_cnvs.csv: - CNVs pre-alignment post-imputation p2preinteg_mcounts.csv: - DNAm beta values sites pre-alignment pre-imputation p2preinteg_dnam_sites.csv: - DNAm beta values sites pre-alignment post-imputation p2preinteg_dnam_dma.csv: - DNAm OLS regression results for weighted average of gene methylation p2preinteg_dnam_genes.csv: - DNAm beta values genes pre-alignment post-imputation p2postinteg_genename_ensembleid_template.csv: - contains annotations for gene names and ensemble ids for integrated data p2postinteg_cnvs_template.csv: - contains annotations for gene names and ensemble ids, as well as for chromosome location, start location, and end location for each gene p2postinteg_raw_rnaseq_counts.csv: - raw counts for differential expression analysis post-alignment p2postinteg_tpm_rnaseq_counts.csv: - TPM counts for SOPA post-alignment p2postinteg_cnvs.csv: - CNVs post-alignment p2postinteg_dnam_genes.csv: - DNAm beta values genes post-alignment p2postinteg_rnaseq_dea.csv: - results of differential expression analysis using log2FC p2postinteg_cnv_da.csv: - results of mutation frequency and significance using Fisher's Exact p2postinteg_dnam_dma.csv: - results of DNAm differential methylation analysis using odds least square regression The GitHub repository connected to these datasets can be found at https://github.com/hasanalsharoh/SIMPA. For utilizing the SOPA/SIMPA tool python package can be found at https://pypi.org/project/SIMPApy/ and the homepage for project at https://github.com/hasanalsharoh/SIMPApy/.本仓库存储了通过单组学单样本通路分析流程（single-omic single-sample pathway analysis pipeline, SOPA）及其整合多组学扩展版本SIMPA所采用的自定义检索标准，从癌症基因组图谱（The Cancer Genome Atlas）获取的全部原始数据。 ### 压缩包文件说明： CNV.rar：包含拷贝数变异（copy number variation, CNV）数据。 RNAseq.rar：包含转录组学数据。 Meth.rar：包含DNA甲基化数据。 SOPA_SIMPA_res.rar：包含基于原始数据计算得到的自定义排序指标所生成的排序结果，运行该流程后得到的SOPA与SIMPA分析结果。 ssGSEA_GDC_res.rar：对基因组数据公共中心（Genomic Data Commons, GDC）样本（n=1968）运行单样本基因集富集分析（single-sample Gene Set Enrichment Analysis, ssGSEA）得到的结果。 GSVA_GDC_res.rar：对GDC样本（n=1968）运行基因集变异分析（Gene Set Variation Analysis, GSVA）得到的结果。 Datasets.rar：包含为开展SOPA/SIMPA的验证与测试所生成的各类分析结果。所有文件均由对应GitHub仓库中的Jupyter Notebook生成，具体结果如下： - clin.csv：包含整合多组学队列的临床信息 - p2preinteg_raw_rnaseq_counts.csv：用于差异表达分析的比对前原始计数数据 - p2preinteg_tpm_rnaseq_counts.csv：比对前每百万转录本（transcripts per million, TPM）计数数据 - p2preinteg_cnv_counts.csv：比对前、插补前的拷贝数变异数据 - p2preinteg_cnvs.csv：比对前、插补后的拷贝数变异数据 - p2preinteg_mcounts.csv：比对前、插补前的DNA甲基化β值位点数据 - p2preinteg_dnam_sites.csv：比对前、插补后的DNA甲基化β值位点数据 - p2preinteg_dnam_dma.csv：用于基因甲基化加权平均的DNA甲基化普通最小二乘（ordinary least squares, OLS）回归分析结果 - p2preinteg_dnam_genes.csv：比对前、插补后的基因水平DNA甲基化β值数据 - p2postinteg_genename_ensembleid_template.csv：包含整合数据的基因名与Ensembl ID注释信息 - p2postinteg_cnvs_template.csv：包含基因名、Ensembl ID，以及各基因的染色体位置、起始位置与终止位置的注释信息 - p2postinteg_raw_rnaseq_counts.csv：用于差异表达分析的比对后原始计数数据 - p2postinteg_tpm_rnaseq_counts.csv：用于SOPA分析的比对后TPM计数数据 - p2postinteg_cnvs.csv：比对后的拷贝数变异数据 - p2postinteg_dnam_genes.csv：比对后的基因水平DNA甲基化β值数据 - p2postinteg_rnaseq_dea.csv：采用log2倍变化（log2FC）进行差异表达分析得到的结果 - p2postinteg_cnv_da.csv：采用Fisher精确检验得到的突变频率与显著性分析结果 - p2postinteg_dnam_dma.csv：采用普通最小二乘回归进行DNA甲基化差异分析得到的结果 本数据集关联的GitHub仓库地址为：https://github.com/hasanalsharoh/SIMPA。 SOPA/SIMPA工具的Python软件包可从https://pypi.org/project/SIMPApy/ 获取，项目主页为https://github.com/hasanalsharoh/SIMPApy/。