Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort

By Sushil Tripathi, Karen R. Christie, R. Balakrishnan, Rachael P. Huntley, David P. Hill, L. Thommesen, Judith A. Blake, Martin Kuiper, A. Lægreid. 2013

60 citations recorded by the source corpus.

Transcription factors control which information in a genome becomes transcribed to produce RNAs that function in the biological systems of cells and organisms. Reliable and comprehensive information about transcription factors is invaluable for large-scale network-based studies. However, existing transcription factor knowledge bases are still lacking in well-documented functional information. Here, we provide guidelines for a curation strategy, which constitutes a robust framework for using the controlled vocabularies defined by the Gene Ontology Consortium to annotate specific DNA binding transcription factors (DbTFs) based on experimental evidence reported in literature. Our standardized protocol and workflow for annotating specific DNA binding RNA polymerase II transcription factors is designed to document high-quality and decisive evidence from valid experimental methods. Within a collaborative biocuration effort involving the user community, we are now in the process of exhaustively annotating the full repertoire of human, mouse and rat proteins that qualify as DbTFs in as much as they are experimentally documented in the biomedical literature today. The completion of this task will significantly enrich Gene Ontology-based information resources for the research community. Database URL: www.tfcheckpoint.org

Subfields: Molecular Biology

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In Molecular Biology

Citations in the corpus

The Gene Ontology Resource: 20 years and still GOing strong (2018, background): “Thetranscription factor areas of GO had previously been refactored between 2010 and 2012 (26,27) with the aim of more finely capturing all combinations of different types of protein and DNA binding activities (e.g. binding to different types of regulatory regions such as promoters and enhancers)…”
Gene Ontology Consortium: going forward (2014, methodology): “org/) has expanded annotation to human, mouse, and rat transcription factors (21), and the Developmental Functional Annotation at Tufts (DFLAT) project improved the quality of annotations of genes involved in fetal development curating human fetal gene functions using both manual and semiautomated a”
Activities at the Universal Protein Resource (UniProt) (2013, unknown): “We also had a successful collaboration with members of the Systems Biology team at NTNU, Mouse Genome Informatics (MGI) and SGD to draw up published guidelines for GO annotation of mammalian transcription factors (14).”