Gene Ontology representation for transcription factor functions.

Journal: Biochimica et biophysica acta. Gene regulatory mechanisms
Published Date: Aug 28, 2021

Abstract

Transcription plays a central role in defining the identity and functionalities of cells, as well as in their responses to changes in the cellular environment. The Gene Ontology (GO) provides a rigorously defined set of concepts that describe the functions of gene products. A GO annotation is a statement about the function of a particular gene product, represented as an association between a gene product and the biological concept a GO term defines. Critically, each GO annotation is based on traceable scientific evidence. Here, we describe the different GO terms that are associated with proteins involved in transcription and its regulation, focusing on the standard of evidence required to support these associations. This article is intended to help users of GO annotations understand how to interpret the annotations and can contribute to the consistency of GO annotations. We distinguish between three classes of activities involved in transcription or directly regulating it - general transcription factors, DNA-binding transcription factors, and transcription co-regulators.

Authors

  • Pascale Gaudet
    Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, Department of Microbiology and Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD, USA, SIB Swiss Institute of Bioinformatics, 1 Rue Michel Servet, 1211 Geneva, Switzerland, Department of Medicine and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD, USA, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA, School of Information, University of South Florida, Tampa, FL, 33647, USA, Genomics Division, Lawrence Berkeley National Lab, 1 Cyclotron Rd., Berkeley, 94720 CA USA, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland, ETH Zurich, Department of Computer Science, Universitätstr. 19, 8092 Zürich, Switzerland, SIB Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zürich, Switzerland and University College London, Gower St, London WC1E 6BT, UK.
  • Colin Logie
    Molecular Biology Department, Faculty of Science, Radboud University, PO box 9101, 6500HB Nijmegen, the Netherlands.
  • Ruth C Lovering
    Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, Rayne Building, 5 University Street, London, WC1E 6JF, UK. r.lovering@ucl.ac.uk.
  • Martin Kuiper
    Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway.
  • Astrid Lægreid
    Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
  • Paul D Thomas
    Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA and.

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