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Bioinformatics. 2014 Oct 15;30(20):2983-5. doi: 10.1093/bioinformatics/btu399. Epub 2014 Jun 23.

TRES predicts transcription control in embryonic stem cells.

Author information

1
The Roslin Institute and Royal (Dick) School of Veterinary Studies, Division of Developmental Biology, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 8GR, UK and Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK.

Abstract

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.

PMID:
24958811
DOI:
10.1093/bioinformatics/btu399
[Indexed for MEDLINE]

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