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.
Highlights
The Gene Ontology (GO) develops a computational model of biological systems, ranging from the molecular to the organism level, across all species in the tree of life
The annotation approach presented here is designed to help biocurators annotate factors involved in transcription and its regulation, as well as for users of GO annotations to understand their meaning and the evidence behind them
This work complements the redesign of this part of the GO to significantly simplify the ontology structure
Summary
Please cite this article as: P. Gaudet, C. Logie, R.C. Lovering, et al, Gene Ontology representation for transcription factor functions, BBA - Gene Regulatory Mechanisms (2021), https://doi.org/10.1016/j.bbagrm.2021.194752 This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Pascale Gaudet1, Colin Logie2, Ruth C. Lovering3, Martin Kuiper4, Astrid Lægreid5, Paul D. Thomas6 Author affiliations:
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