Additional file 18 of Gene networks and transcriptional regulators associated with liver cancer development and progression

Additional file 18. Lists of overrepresented transcription factor binding sites (TFBSs) in genes downregulated in GE2-hepatocellular carcinoma (HCC). Significantly down regulated genes in GE2-HCC (n=13) versus NT (n=17) samples with mean fold change (FC) ≤ -2 and false discovery rate (FDR) ≤ 0.05 (Additional file 5) were used as an input gene list for bioinformatics analyses. Promoter sequences of the co-regulated in tumours genes (“Yes” set) and the control gene set (“No” set) were searched for potential transcription factor binding sites (TFBSs) using the MATCHTM tool and TRANSFAC® library of positional weight matrices. The frequencies of TFBSs in the “Yes” gene set and “No” gene set were identified, and the ratio of “Yes” versus “No” was calculated. Yes/No ratio > 1 indicates overrepresentation of TFBSs in the co-regulated genes and suggests potential involvement of the corresponding transcription factor in regulation of the observed expression changes.

附加文件18：GE2型肝细胞癌（hepatocellular carcinoma, HCC）中下调基因内过度富集的转录因子结合位点（transcription factor binding sites, TFBSs）列表。本研究选取GE2-HCC（n=13）与正常组织（NT，n=17）样本中显著下调的基因作为输入基因列表开展生物信息学分析，该类基因需满足平均折叠变化（mean fold change, FC）≤-2且错误发现率（false discovery rate, FDR）≤0.05的筛选条件，相关基因列表详见附加文件5。采用MATCH™工具及TRANSFAC®位置权重矩阵库，对肿瘤共调控基因集合（“Yes”组）与对照基因集合（“No”组）的启动子序列进行潜在转录因子结合位点（TFBSs）检索。统计“Yes”组与“No”组中TFBSs的出现频率，并计算两组的频率比值。若“Yes”组与“No”组的比值>1，则表明该转录因子结合位点在共调控基因中存在富集，提示对应转录因子可能参与了本次观测到的基因表达调控变化。