title: TRES predicts transcription control in embryonic stem cells.
abstract: CONCLUSIONS
  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.
  
  
  METHODS
  TRES is freely available at http://www.tres.roslin.ed.ac.uk.
  
  
  BACKGROUND
  Anagha.Joshi@roslin.ed.ac.uk or bg200@cam.ac.uk
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: 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.
authors: Christopher
authors: C
authors: Pooley
authors: 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.
authors: David
authors: D
authors: Ruau
authors: 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.
authors: Patrick
authors: P
authors: Lombard
authors: 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.
authors: Berthold
authors: B
authors: Gottgens
authors: 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.
authors: Anagha
authors: A
authors: Joshi
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods*; D053595:Embryonic Stem Cells / Q000378:metabolism*; D005786:Gene Expression Regulation; D006801:Humans; D020407:Internet; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D017421:Sequence Analysis; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D014157:Transcription Factors