Data for "Challenges and Opportunities in Single-Sample Network Modeling"

This repository stores the data that were used as the basis for the analyses in "Challenges and Opportunities for Single Sample Network Modeling". Corresponding code can be found at https://github.com/kimberlyglass/single-sample-networks. To easily run the github code, the three files in this repository should be added into the "Data" directory and "GTExData.zip" should be un-zipped. The files included in this repository include: (1) InSilicoData.mat -- a "mat" file containing generated data for 6 genes and 600 samples based on three known network structures (250 in sample set 1, 250 in sample set 2, and 100 in sample set 3). Used for the "toy data" analysis and created using MakeInSilicoData.m. This file stores the following variables: -- 'ExpData': a 6 by 600 matrix containing simulated gene expression values. -- 'SSNets': a 6 element cell array. Each element contains a 15 by 600 matrix with the inferred edge weights for each sample based on applying six different single-sample network modeling approaches: LIONESS::PCC, SSN, SWEET, BONOBO, LIONESS::MI, CSN. -- 'numsampOrg': the number of samples in sample set 1 (one clique) and in sample set 2 (two cliques); value is 250. -- 'numsampRnd': the number of "noisy" samples in sample set 3; value is 100. -- 'NodeIdx': a 6-choose-2 = 15 by 2 matrix with the edge information for the inferred single-sample networks. (2) GTEx_MixData3.mat -- a "mat" file containing gene expression data for 250 samples in each of 15 different tissues. The 13281 genes in these data are protein-coding genes with a median expression of at least 2 in all 15 tissues. Used for the GTEx / human data analysis and created using MakeGTEx_MixData3.m. This file stores the following variables: -- 'ExpData': a 13281 by 3750 matrix containg gene expression values from GTEx. -- 'GeneSymbols': the names of genes in the rows of 'ExpData' -- 'Tissue': the tissues for the samples in the columns of 'ExpData' (3) GTExData.zip -- a zip of the "GTExData" subdirectory, which contains GTEx data files that were parsed to create the GTEx_MaxData3.mat file. These files include: -- GTEx_NormExpressionData.txt: a file containing gene expression data from GTEx, processed as described in PMID#29069589. -- GTEx_AnnInfo_AllGenes.txt: a file containing information about the genes in "GTEx_NormExpressionData.txt" -- GTEx_SampleInfo.txt: a file containing information about the samples in "GTEx_NormExpressionData.txt"本仓库存储了支撑《单样本网络建模的挑战与机遇》（Challenges and Opportunities for Single Sample Network Modeling）一文分析工作的基础数据集。对应的代码可在https://github.com/kimberlyglass/single-sample-networks 获取。 若需便捷运行该GitHub仓库中的代码，请将本仓库内的三个文件添加至程序的"Data"目录中，并解压"GTExData.zip"文件。 本仓库包含的文件如下： (1) InSilicoData.mat：MATLAB格式数据文件（mat file），基于三种已知网络结构生成了涵盖6个基因、600个样本的模拟数据（样本集1含250个样本，样本集2含250个样本，样本集3含100个样本），用于“玩具数据集（toy data）”分析，由MakeInSilicoData.m脚本生成。该文件存储以下变量： -- "ExpData"：6×600矩阵，存储模拟的基因表达值。 -- "SSNets"：包含6个元素的元胞数组（cell array），每个元素为15×600矩阵，对应基于6种不同单样本网络建模方法：LIONESS::PCC、SSN、SWEET、BONOBO、LIONESS::MI、CSN，推断得到的各样本边权重矩阵。 -- "numsampOrg"：样本集1（单个团簇（clique））和样本集2（两个团簇）的样本量，取值为250。 -- "numsampRnd"：样本集3中“带噪声”样本的数量，取值为100。 -- "NodeIdx"：15×2矩阵，存储推断得到的单样本网络的边信息（15为6选2的组合数）。 (2) GTEx_MixData3.mat：MATLAB格式数据文件（mat file），包含15种不同组织各250个样本的基因表达数据。该数据集的13281个基因为蛋白编码基因，且在全部15种组织中的中位表达量不低于2，用于GTEx/人类数据集分析，由MakeGTEx_MixData3.m脚本生成。该文件存储以下变量： -- "ExpData"：13281×3750矩阵，存储来自GTEx的基因表达值。 -- "GeneSymbols"："ExpData"矩阵各行对应的基因符号。 -- "Tissue"："ExpData"矩阵各列对应的样本所属组织。 (3) GTExData.zip："GTExData"子目录的压缩包，该子目录包含用于生成GTEx_MaxData3.mat文件的原始GTEx数据文件，具体包括： -- GTEx_NormExpressionData.txt：存储来自GTEx的基因表达数据，处理流程遵循PMID#29069589文献中的方法。 -- GTEx_AnnInfo_AllGenes.txt：存储"GTEx_NormExpressionData.txt"中涉及的基因相关信息。 -- GTEx_SampleInfo.txt：存储"GTEx_NormExpressionData.txt"中涉及的样本相关信息。