Cargando…
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...
Autores principales: | , , , , , , , |
---|---|
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 |
_version_ | 1782490900741488640 |
---|---|
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. |
format | Online Article Text |
id | pubmed-5210527 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT lishujing cgdbadatabaseofcircadiangenesineukaryotes AT shuike cgdbadatabaseofcircadiangenesineukaryotes AT zhangying cgdbadatabaseofcircadiangenesineukaryotes AT lvyongqiang cgdbadatabaseofcircadiangenesineukaryotes AT dengwankun cgdbadatabaseofcircadiangenesineukaryotes AT ullahshahid cgdbadatabaseofcircadiangenesineukaryotes AT zhangluoying cgdbadatabaseofcircadiangenesineukaryotes AT xueyu cgdbadatabaseofcircadiangenesineukaryotes |