Identification of transcription factors (TFs) and targets involved in the cholangiocarcinoma (CCA) by integrated analysis.

The present study was designed to investigate the upstream transcription factors (TFs) and the signature genes in cholangiocarcinoma (CCA), providing better clues on the regulatory mechanisms and therapeutic applications. Gene expression data sets of CCA were searched in the Gene Expression Omnibus database for integrated analysis. Functional annotation of differently expressed genes (DEGs) was then conducted and the TFs were identified. Moreover, a global transcriptional regulatory network of TFs-targets was constructed. Integrated analysis of five eligible Gene Expression Omnibus data sets led to a set of 993 DEGs and 48 TFs in CCA. The constructed TFs-targets regulatory network consisted of 697 TF-target interactions between 41 TFs and 436 DEGs. The top 10 TFs covering the most downstream DEGs were NFATC2, SOX10, ARID3A, ZNF263, NR4A2, GATA3, EGR1, PLAG1, STAT3 and FOSL1, which may have important roles in the tumorigenesis of CCA. Supporting the fact that defects of cell-cycle surveillance mechanism were closely related to various cancers, we found that cell cycle was the most significantly enriched pathway. KCNN2 and ADCY6 were involved in the bile secretion. Thus, their aberrant expression may be closely related to the pathogenesis of CCA. Particularly, we found that upregulation of EZH2 in CCA is a powerful potential marker for CCA.