Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort.
Document Type
Article
Publication Date
8-27-2013
JAX Source
Database (Oxford) 2013 Aug 27; 2013:bat062
Volume
2013
First Page
062
Last Page
062
ISSN
1758-0463
PMID
23981286
Abstract
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. Database (Oxford) 2013 Aug 27; 2013:bat062
Recommended Citation
Tripathi S,
Christie KR,
Balakrishnan R,
Huntley R,
Hill DP,
Thommesen L,
Blake JA,
Kuiper M,
Lægreid A.
Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort. Database (Oxford) 2013 Aug 27; 2013:bat062