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CGDB: a database of circadian genes in eukaryotes

We report a database of circadian genes in eukaryotes (CGDB, http://cgdb.biocuckoo.org), containing ∼73 000 circadian-related genes in 68 animals, 39 plants and 41 fungi. Circadian rhythm is ∼24 h rhythm in behavioral and physiological processes that exists in almost all organisms on the earth. Defe...

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Autores principales: Li, Shujing, Shui, Ke, Zhang, Ying, Lv, Yongqiang, Deng, Wankun, Ullah, Shahid, Zhang, Luoying, Xue, Yu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210527/
https://www.ncbi.nlm.nih.gov/pubmed/27789706
http://dx.doi.org/10.1093/nar/gkw1028
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author Li, Shujing
Shui, Ke
Zhang, Ying
Lv, Yongqiang
Deng, Wankun
Ullah, Shahid
Zhang, Luoying
Xue, Yu
author_facet Li, Shujing
Shui, Ke
Zhang, Ying
Lv, Yongqiang
Deng, Wankun
Ullah, Shahid
Zhang, Luoying
Xue, Yu
author_sort Li, Shujing
collection PubMed
description We report a database of circadian genes in eukaryotes (CGDB, http://cgdb.biocuckoo.org), containing ∼73 000 circadian-related genes in 68 animals, 39 plants and 41 fungi. Circadian rhythm is ∼24 h rhythm in behavioral and physiological processes that exists in almost all organisms on the earth. Defects in the circadian system are highly associated with a number of diseases such as cancers. Although several databases have been established for rhythmically expressed genes, a comprehensive database of cycling genes across phyla is still lacking. From the literature, we collected 1382 genes of which transcript level oscillations were validated using methods such as RT-PCR, northern blot and in situ hybridization. Given that many genes exhibit different oscillatory patterns in different tissues/cells within an organism, we have included information regarding the phase and amplitude of the oscillation, as well as the tissue/cells in which the oscillation was identified. Using these well characterized cycling genes, we have then conducted an orthologous search and identified ∼45 000 potential cycling genes from 148 eukaryotes. Given that significant effort has been devoted to identifying cycling genes by transcriptome profiling, we have also incorporated these results, a total of over 26 000 genes, into our database.
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spelling pubmed-52105272017-01-05 CGDB: a database of circadian genes in eukaryotes Li, Shujing Shui, Ke Zhang, Ying Lv, Yongqiang Deng, Wankun Ullah, Shahid Zhang, Luoying Xue, Yu Nucleic Acids Res Database Issue We report a database of circadian genes in eukaryotes (CGDB, http://cgdb.biocuckoo.org), containing ∼73 000 circadian-related genes in 68 animals, 39 plants and 41 fungi. Circadian rhythm is ∼24 h rhythm in behavioral and physiological processes that exists in almost all organisms on the earth. Defects in the circadian system are highly associated with a number of diseases such as cancers. Although several databases have been established for rhythmically expressed genes, a comprehensive database of cycling genes across phyla is still lacking. From the literature, we collected 1382 genes of which transcript level oscillations were validated using methods such as RT-PCR, northern blot and in situ hybridization. Given that many genes exhibit different oscillatory patterns in different tissues/cells within an organism, we have included information regarding the phase and amplitude of the oscillation, as well as the tissue/cells in which the oscillation was identified. Using these well characterized cycling genes, we have then conducted an orthologous search and identified ∼45 000 potential cycling genes from 148 eukaryotes. Given that significant effort has been devoted to identifying cycling genes by transcriptome profiling, we have also incorporated these results, a total of over 26 000 genes, into our database. Oxford University Press 2017-01-04 2016-10-26 /pmc/articles/PMC5210527/ /pubmed/27789706 http://dx.doi.org/10.1093/nar/gkw1028 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Database Issue
Li, Shujing
Shui, Ke
Zhang, Ying
Lv, Yongqiang
Deng, Wankun
Ullah, Shahid
Zhang, Luoying
Xue, Yu
CGDB: a database of circadian genes in eukaryotes
title CGDB: a database of circadian genes in eukaryotes
title_full CGDB: a database of circadian genes in eukaryotes
title_fullStr CGDB: a database of circadian genes in eukaryotes
title_full_unstemmed CGDB: a database of circadian genes in eukaryotes
title_short CGDB: a database of circadian genes in eukaryotes
title_sort cgdb: a database of circadian genes in eukaryotes
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210527/
https://www.ncbi.nlm.nih.gov/pubmed/27789706
http://dx.doi.org/10.1093/nar/gkw1028
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