TRES predicts transcription control in embryonic stem cells.
Oxford University Press (OUP)
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Pooley, C., Ruau, D., Lombard, P., Gottgens, B., & Joshi, A. (2014). TRES predicts transcription control in embryonic stem cells.. Bioinformatics https://doi.org/10.1093/bioinformatics/btu399
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 firstname.lastname@example.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
This work was supported by a University of Edinburgh Chancellors Fellowship awarded to AJ and strategic funding from the BBSRC. CP was funded by the Scottish Government through the Strategic Partnership for Animal Science Excellence (SPASE). The Gottgens’ lab is supported by LLR, the MRC, BBSRC, Cancer Research UK, and Wellcome Trust core support to the Cambridge Institute for Medical Research and Wellcome Trust–MRC Cambridge Stem Cell Institute.
Cancer Research Uk (None)
Biotechnology and Biological Sciences Research Council (BB/I00050X/1)
Leukaemia & Lymphoma Research (12029)
Wellcome Trust (097922/Z/11/Z)
Medical Research Council (MC_PC_12009)
Leukemia & Lymphoma Society (7001-12)
National Centre for the Replacement Refinement and Reduction of Animals in Research (G0900729/1)
External DOI: https://doi.org/10.1093/bioinformatics/btu399
This record's URL: https://www.repository.cam.ac.uk/handle/1810/245448