MOESM1 of Integrated genomic characterization of cancer genes in glioma

Additional file 1: Figure S1. Driver genes in IDH1-mutated, non-IDH1-mutated and total glioma groups. A. The overlap of driver genes predicted by OncodriveCLUST in the three groups; B. The overlap of driver genes predicted by OncodriveFM in the three groups; C. The overlap of driver genes predicted by Icages in the three groups; D. The overlap of driver genes predicted by Drgap in the three groups; E. The overlap of driver genes predicted by Dendrix in the three groups; F. The overlap of driver pathways predicted by Dendrix in the three groups. Figure S2. Expression profiling of 428 driver genes between glioma and normal brain samples, expression values of each gene was presented as log(FPKM + 0.001). Figure S3. The protein–protein interaction network of driver genes. Network nodes represent proteins, network edges represent protein–protein associations. Notably, disconnected nodes were disabled in the network. Colored nodes refer to query proteins and first shell of interactors, white nodes are second shell of interactors. Blue lines represent known interactions from curated Kyoto Encyclopedia of Genes and Genomes database. Pink lines represent experimentally determined protein–protein interactions. Green lines denote genes that are frequently observed in each other’s genomic neighborhood. Black lines stand for genes whose expression is correlated across a large number of experiments. Dark blue gene families show similar occurrence patterns across genomes, light blue proteins show amino acid sequence similarity. Figure S4. The frequencies of copy number variations in 52 glioma samples.

附加文件1：图S1。异柠檬酸脱氢酶1（IDH1）突变型、非IDH1突变型及总体胶质瘤组中的驱动基因。A. 三个组别中经OncodriveCLUST预测得到的驱动基因的重叠情况；B. 三个组别中经OncodriveFM预测得到的驱动基因的重叠情况；C. 三个组别中经Icages预测得到的驱动基因的重叠情况；D. 三个组别中经Drgap预测得到的驱动基因的重叠情况；E. 三个组别中经Dendrix预测得到的驱动基因的重叠情况；F. 三个组别中经Dendrix预测得到的驱动通路的重叠情况。
图S2：428个驱动基因在胶质瘤样本与正常脑组织样本中的表达谱，每个基因的表达值以log(FPKM + 0.001)形式呈现，其中FPKM为每百万映射读段的每千碱基转录本片段数（Fragments Per Kilobase of transcript per Million mapped reads）。
图S3：驱动基因的蛋白质相互作用网络。网络节点代表蛋白质，网络边代表蛋白质间的相互关联。需注意的是，该网络未纳入孤立节点。着色节点代表查询蛋白及其互作第一邻层，白色节点代表互作第二邻层。蓝色线条代表源自经人工整理的京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes，KEGG）数据库的已知相互作用；粉色线条代表经实验验证的蛋白质相互作用；绿色线条代表彼此在基因组邻区中频繁共现的基因；黑色线条代表在大量实验中表达模式存在相关性的基因；深蓝色基因家族代表在不同基因组中具有相似的出现模式；浅蓝色蛋白质代表具有氨基酸序列相似性的蛋白质。
图S4：52例胶质瘤样本的拷贝数变异频率。