Function Annotation of an SBP-box Gene in Arabidopsis Based on Analysis of Co-expression Networks and Promoters
The SQUAMOSA PROMOTER BINDING PROTEIN–LIKE (SPL) gene family is an SBP-box transcription family in Arabidopsis. While several physiological responses to SPL genes have been reported, their biological role remains elusive. Here, we use a combined analysis of expression correlation, the interacto...
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| Format: | Article |
| Language: | English |
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MDPI AG
2009-01-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | http://www.mdpi.com/1422-0067/10/1/116/ |
| _version_ | 1811263823977381888 |
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| author | Yi Wang Yuxin Yang Zongli Hu Guoping Chen Xuqing Chen |
| author_facet | Yi Wang Yuxin Yang Zongli Hu Guoping Chen Xuqing Chen |
| author_sort | Yi Wang |
| collection | DOAJ |
| description | The SQUAMOSA PROMOTER BINDING PROTEIN–LIKE (SPL) gene family is an SBP-box transcription family in Arabidopsis. While several physiological responses to SPL genes have been reported, their biological role remains elusive. Here, we use a combined analysis of expression correlation, the interactome, and promoter content to infer the biological role of the SPL genes in Arabidopsis thaliana. Analysis of the SPL-correlated gene network reveals multiple functions for SPL genes. Network analysis shows that SPL genes function by controlling other transcription factor families and have relatives with membrane protein transport activity. The interactome analysis of the correlation genes suggests that SPL genes also take part in metabolism of glucose, inorganic salts, and ATP production. Furthermore, the promoters of the correlated genes contain a core binding cis-element (GTAC). All of these analyses suggest that SPL genes have varied functions in Arabidopsis. |
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| id | doaj.art-7f6c8fe717784bfa9b265832cbff10a5 |
| institution | Directory Open Access Journal |
| issn | 1422-0067 |
| language | English |
| last_indexed | 2024-04-12T19:52:01Z |
| publishDate | 2009-01-01 |
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| spelling | doaj.art-7f6c8fe717784bfa9b265832cbff10a52022-12-22T03:18:47ZengMDPI AGInternational Journal of Molecular Sciences1422-00672009-01-0110111613210.3390/ijms10010116Function Annotation of an SBP-box Gene in Arabidopsis Based on Analysis of Co-expression Networks and PromotersYi WangYuxin YangZongli HuGuoping ChenXuqing ChenThe SQUAMOSA PROMOTER BINDING PROTEIN–LIKE (SPL) gene family is an SBP-box transcription family in Arabidopsis. While several physiological responses to SPL genes have been reported, their biological role remains elusive. Here, we use a combined analysis of expression correlation, the interactome, and promoter content to infer the biological role of the SPL genes in Arabidopsis thaliana. Analysis of the SPL-correlated gene network reveals multiple functions for SPL genes. Network analysis shows that SPL genes function by controlling other transcription factor families and have relatives with membrane protein transport activity. The interactome analysis of the correlation genes suggests that SPL genes also take part in metabolism of glucose, inorganic salts, and ATP production. Furthermore, the promoters of the correlated genes contain a core binding cis-element (GTAC). All of these analyses suggest that SPL genes have varied functions in Arabidopsis.http://www.mdpi.com/1422-0067/10/1/116/ArabidopsisSPLco-expressionnetworkpromoter |
| spellingShingle | Yi Wang Yuxin Yang Zongli Hu Guoping Chen Xuqing Chen Function Annotation of an SBP-box Gene in Arabidopsis Based on Analysis of Co-expression Networks and Promoters International Journal of Molecular Sciences Arabidopsis SPL co-expression network promoter |
| title | Function Annotation of an SBP-box Gene in Arabidopsis Based on Analysis of Co-expression Networks and Promoters |
| title_full | Function Annotation of an SBP-box Gene in Arabidopsis Based on Analysis of Co-expression Networks and Promoters |
| title_fullStr | Function Annotation of an SBP-box Gene in Arabidopsis Based on Analysis of Co-expression Networks and Promoters |
| title_full_unstemmed | Function Annotation of an SBP-box Gene in Arabidopsis Based on Analysis of Co-expression Networks and Promoters |
| title_short | Function Annotation of an SBP-box Gene in Arabidopsis Based on Analysis of Co-expression Networks and Promoters |
| title_sort | function annotation of an sbp box gene in arabidopsis based on analysis of co expression networks and promoters |
| topic | Arabidopsis SPL co-expression network promoter |
| url | http://www.mdpi.com/1422-0067/10/1/116/ |
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