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mTFkb: a knowledgebase for fundamental annotation of mouse transcription factors

Transcription factors (TFs) are well-known important regulators in cell biology and tissue development. However, in mouse, one of the most widely-used model species, currently the vast majority of the known TFs have not been functionally studied due to the lack of sufficient annotations. To this end...

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Autores principales: Sun, Kun, Wang, Huating, Sun, Hao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5465081/
https://www.ncbi.nlm.nih.gov/pubmed/28596516
http://dx.doi.org/10.1038/s41598-017-02404-w
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author Sun, Kun
Wang, Huating
Sun, Hao
author_facet Sun, Kun
Wang, Huating
Sun, Hao
author_sort Sun, Kun
collection PubMed
description Transcription factors (TFs) are well-known important regulators in cell biology and tissue development. However, in mouse, one of the most widely-used model species, currently the vast majority of the known TFs have not been functionally studied due to the lack of sufficient annotations. To this end, we collected and analyzed the whole transcriptome sequencing data from more than 30 major mouse tissues and used the expression profiles to annotate the TFs. We found that the expression patterns of the TFs are highly correlated with the histology of the tissue types thus can be used to infer the potential functions of the TFs. Furthermore, we found that as many as 30% TFs display tissue-specific expression pattern, and these tissue-specific TFs are among the key TFs in their corresponding tissues. We also observed signals of divergent transcription associated with many TFs with unique expression pattern. Lastly, we have integrated all the data, our analysis results as well as various annotation resources to build a web-based database named mTFkb freely accessible at http://www.myogenesisdb.org/mTFkb/. We believe that mTFkb could serve as a useful and valuable resource for TF studies in mouse.
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spelling pubmed-54650812017-06-14 mTFkb: a knowledgebase for fundamental annotation of mouse transcription factors Sun, Kun Wang, Huating Sun, Hao Sci Rep Article Transcription factors (TFs) are well-known important regulators in cell biology and tissue development. However, in mouse, one of the most widely-used model species, currently the vast majority of the known TFs have not been functionally studied due to the lack of sufficient annotations. To this end, we collected and analyzed the whole transcriptome sequencing data from more than 30 major mouse tissues and used the expression profiles to annotate the TFs. We found that the expression patterns of the TFs are highly correlated with the histology of the tissue types thus can be used to infer the potential functions of the TFs. Furthermore, we found that as many as 30% TFs display tissue-specific expression pattern, and these tissue-specific TFs are among the key TFs in their corresponding tissues. We also observed signals of divergent transcription associated with many TFs with unique expression pattern. Lastly, we have integrated all the data, our analysis results as well as various annotation resources to build a web-based database named mTFkb freely accessible at http://www.myogenesisdb.org/mTFkb/. We believe that mTFkb could serve as a useful and valuable resource for TF studies in mouse. Nature Publishing Group UK 2017-06-08 /pmc/articles/PMC5465081/ /pubmed/28596516 http://dx.doi.org/10.1038/s41598-017-02404-w Text en © The Author(s) 2017 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Sun, Kun
Wang, Huating
Sun, Hao
mTFkb: a knowledgebase for fundamental annotation of mouse transcription factors
title mTFkb: a knowledgebase for fundamental annotation of mouse transcription factors
title_full mTFkb: a knowledgebase for fundamental annotation of mouse transcription factors
title_fullStr mTFkb: a knowledgebase for fundamental annotation of mouse transcription factors
title_full_unstemmed mTFkb: a knowledgebase for fundamental annotation of mouse transcription factors
title_short mTFkb: a knowledgebase for fundamental annotation of mouse transcription factors
title_sort mtfkb: a knowledgebase for fundamental annotation of mouse transcription factors
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5465081/
https://www.ncbi.nlm.nih.gov/pubmed/28596516
http://dx.doi.org/10.1038/s41598-017-02404-w
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