Summary: 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.
Availability And Implementation: TRES is freely available at http://www.tres.roslin.ed.ac.uk.
Contact: Anagha.Joshi@roslin.ed.ac.uk or bg200@cam.ac.uk
Supplementary Information: Supplementary data are available at Bioinformatics online.
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| http://dx.doi.org/10.1093/bioinformatics/btu399 | DOI Listing |
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