ProFITS of maize: a database of protein families involved in the transduction of signalling in the maize genome
<p>Abstract</p> <p>Background</p> <p>Maize (<it>Zea mays </it>ssp. <it>mays </it>L.) is an important model for plant basic and applied research. In 2009, the B73 maize genome sequencing made a great step forward, using clone by clone strategy; ho...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2010-10-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/11/580 |
| _version_ | 1811266941600399360 |
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| author | Zhang Zhenhai Du Zhou Ling Yi Su Zhen |
| author_facet | Zhang Zhenhai Du Zhou Ling Yi Su Zhen |
| author_sort | Zhang Zhenhai |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Maize (<it>Zea mays </it>ssp. <it>mays </it>L.) is an important model for plant basic and applied research. In 2009, the B73 maize genome sequencing made a great step forward, using clone by clone strategy; however, functional annotation and gene classification of the maize genome are still limited. Thus, a well-annotated datasets and informative database will be important for further research discoveries. Signal transduction is a fundamental biological process in living cells, and many protein families participate in this process in sensing, amplifying and responding to various extracellular or internal stimuli. Therefore, it is a good starting point to integrate information on the maize functional genes involved in signal transduction.</p> <p>Results</p> <p>Here we introduce a comprehensive database 'ProFITS' (Protein Families Involved in the Transduction of Signalling), which endeavours to identify and classify protein kinases/phosphatases, transcription factors and ubiquitin-proteasome-system related genes in the B73 maize genome. Users can explore gene models, corresponding transcripts and FLcDNAs using the three abovementioned protein hierarchical categories, and visualize them using an AJAX-based genome browser (JBrowse) or Generic Genome Browser (GBrowse). Functional annotations such as GO annotation, protein signatures, protein best-hits in the <it>Arabidopsis </it>and rice genome are provided. In addition, pre-calculated transcription factor binding sites of each gene are generated and mutant information is incorporated into ProFITS. In short, ProFITS provides a user-friendly web interface for studies in signal transduction process in maize.</p> <p>Conclusion</p> <p>ProFITS, which utilizes both the B73 maize genome and full length cDNA (FLcDNA) datasets, provides users a comprehensive platform of maize annotation with specific focus on the categorization of families involved in the signal transduction process. ProFITS is designed as a user-friendly web interface and it is valuable for experimental researchers. It is freely available now to all users at <url>http://bioinfo.cau.edu.cn/ProFITS</url>.</p> |
| first_indexed | 2024-04-12T20:52:22Z |
| format | Article |
| id | doaj.art-5bf009743348425ca2673008c6dc7c4e |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-12T20:52:22Z |
| publishDate | 2010-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-5bf009743348425ca2673008c6dc7c4e2022-12-22T03:17:04ZengBMCBMC Genomics1471-21642010-10-0111158010.1186/1471-2164-11-580ProFITS of maize: a database of protein families involved in the transduction of signalling in the maize genomeZhang ZhenhaiDu ZhouLing YiSu Zhen<p>Abstract</p> <p>Background</p> <p>Maize (<it>Zea mays </it>ssp. <it>mays </it>L.) is an important model for plant basic and applied research. In 2009, the B73 maize genome sequencing made a great step forward, using clone by clone strategy; however, functional annotation and gene classification of the maize genome are still limited. Thus, a well-annotated datasets and informative database will be important for further research discoveries. Signal transduction is a fundamental biological process in living cells, and many protein families participate in this process in sensing, amplifying and responding to various extracellular or internal stimuli. Therefore, it is a good starting point to integrate information on the maize functional genes involved in signal transduction.</p> <p>Results</p> <p>Here we introduce a comprehensive database 'ProFITS' (Protein Families Involved in the Transduction of Signalling), which endeavours to identify and classify protein kinases/phosphatases, transcription factors and ubiquitin-proteasome-system related genes in the B73 maize genome. Users can explore gene models, corresponding transcripts and FLcDNAs using the three abovementioned protein hierarchical categories, and visualize them using an AJAX-based genome browser (JBrowse) or Generic Genome Browser (GBrowse). Functional annotations such as GO annotation, protein signatures, protein best-hits in the <it>Arabidopsis </it>and rice genome are provided. In addition, pre-calculated transcription factor binding sites of each gene are generated and mutant information is incorporated into ProFITS. In short, ProFITS provides a user-friendly web interface for studies in signal transduction process in maize.</p> <p>Conclusion</p> <p>ProFITS, which utilizes both the B73 maize genome and full length cDNA (FLcDNA) datasets, provides users a comprehensive platform of maize annotation with specific focus on the categorization of families involved in the signal transduction process. ProFITS is designed as a user-friendly web interface and it is valuable for experimental researchers. It is freely available now to all users at <url>http://bioinfo.cau.edu.cn/ProFITS</url>.</p>http://www.biomedcentral.com/1471-2164/11/580 |
| spellingShingle | Zhang Zhenhai Du Zhou Ling Yi Su Zhen ProFITS of maize: a database of protein families involved in the transduction of signalling in the maize genome BMC Genomics |
| title | ProFITS of maize: a database of protein families involved in the transduction of signalling in the maize genome |
| title_full | ProFITS of maize: a database of protein families involved in the transduction of signalling in the maize genome |
| title_fullStr | ProFITS of maize: a database of protein families involved in the transduction of signalling in the maize genome |
| title_full_unstemmed | ProFITS of maize: a database of protein families involved in the transduction of signalling in the maize genome |
| title_short | ProFITS of maize: a database of protein families involved in the transduction of signalling in the maize genome |
| title_sort | profits of maize a database of protein families involved in the transduction of signalling in the maize genome |
| url | http://www.biomedcentral.com/1471-2164/11/580 |
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