{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T06:07:22Z","timestamp":1674886042467},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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 \u2018TRES\u2019 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.<\/jats:p>\n               <jats:p>Availability and implementation: TRES is freely available at http:\/\/www.tres.roslin.ed.ac.uk .<\/jats:p>\n               <jats:p>Contact: \u00a0Anagha.Joshi@roslin.ed.ac.uk or bg200@cam.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu399","type":"journal-article","created":{"date-parts":[[2014,6,24]],"date-time":"2014-06-24T06:29:49Z","timestamp":1403591389000},"page":"2983-2985","source":"Crossref","is-referenced-by-count":3,"title":["TRES predicts transcription control in embryonic stem cells"],"prefix":"10.1093","volume":"30","author":[{"given":"Christopher","family":"Pooley","sequence":"first","affiliation":[{"name":"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 2 Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Ruau","sequence":"additional","affiliation":[{"name":"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 2 Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrick","family":"Lombard","sequence":"additional","affiliation":[{"name":"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 2 Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Berthold","family":"Gottgens","sequence":"additional","affiliation":[{"name":"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 2 Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anagha","family":"Joshi","sequence":"additional","affiliation":[{"name":"1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, Division of Developmental Biology, University of Edinburgh, Easter Bush 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