TRES predicts transcription control in embryonic stem cells.

Abstract

Unraveling transcriptional circuits controlling embryonic stem cell maintenance and fate has great potential for improving our understanding of normal development as well as disease. To facilitate this, we have developed a novel web tool called 'TRES' that predicts the likely upstream regulators for a given gene list. This is achieved by integrating transcription factor (TF) binding events from 187 ChIP-sequencing and ChIP-on-chip datasets in murine and human embryonic stem (ES) cells with over 1000 mammalian TF sequence motifs. Using 114 TF perturbation gene sets, as well as 115 co-expression clusters in ES cells, we validate the utility of this approach. TRES is freely available at http://www.tres.roslin.ed.ac.uk. Anagha.Joshi@roslin.ed.ac.uk or bg200@cam.ac.uk Supplementary data are available at Bioinformatics online.