Identification of Pou5f1 , Sox2 , and Nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data

摘要: Target genes of a transcription factor (TF) Pou5f1 (Oct3/4 or Oct4), which is essential for pluripotency maintenance and self-renewal embryonic stem (ES) cells, have previously been identified based on their response to manipulation occurrence Chromatin-immunoprecipitation (ChIP)-binding sites in promoters. However, many responding with binding may not be direct targets because mediated by other ChIP-binding site functional terms regulation. To reduce the number false positives, we propose separate into groups according direction, magnitude, time response, apply discovery rate (FDR) criterion each group individually. Using this novel algorithm stringent statistical criteria (FDR < 0.2) compendium published new microarray data (3, 6, 12, 24 hr after suppression) ChIP data, 420 tentative target (TTGs) Pou5f1. The majority TTGs (372) were down-regulated suppression, indicating that functions as an activator gene expression when it binds Interestingly, activated are potent suppressors transcription, include polycomb genes, zinc finger TFs, chromatin remodeling factors, signaling. Similar analysis showed Sox2 Nanog also function mostly activators cooperation We most reliable sets key – Pou5f1, Sox2, Nanog, found they predominantly downstream expression. Thus, related cell differentiation suppressed indirectly.