Additional file 16 of Gene networks and transcriptional regulators associated with liver cancer development and progression

Additional file 16. Lists of overrepresented transcription factor binding sites (TFBSs) in genes upregulated in GE2-hepatocellular carcinoma (HCC). Significantly up 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.