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

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

Sushil Tripathi et al. Database (Oxford). 2013.

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.

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Figures

Figure 1.

Figure 1.

Primary GO terms/subgraphs used for DbTF annotation. (A) GO subgraph used for sequence-specific DbTF. In this graph, sequence-specific DNA binding MF terms (yellow), sequence-specific DNA binding TF activity MF terms (green) and transcription regulation BP (blue) are shown along with the relationships between terms in the graph structure. (B) GO subgraph used for transcription factor binding transcription factors. In this graph, the different color coding represents the following: TF binding MF terms (yellow), transcription regulation BP (blue) and TF binding TF activity MF terms (green). I, P and H on top of the lines stand for relationships ‘is_a’, ‘part_of’ and ‘has_part’.

Figure 2.

Figure 2.

Sequence-specific DNA binding TF (DbTF) curation workflow. This workflow represents the step-by-step procedure for curating experimentally verified mammalian DbTFs from scientific publications. Selection of scientific publication from the literature corpus is the starting point of the curation procedure. From each relevant publication, DbTF-specific GO-terms are annotated and recorded.

Figure 3.

Figure 3.

UniProt-GOA screenshot of some of the DbTF annotations. The annotations generated using the DbTF curation guidelines discussed here can be accessed from the GO database using the QuickGO tool.

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