Function Annotation of an SBP-box Gene in Arabidopsis Based on Analysis of Co-expression Networks and Promoters
Open Access
- 2 January 2009
- journal article
- research article
- Published by MDPI AG in International Journal of Molecular Sciences
- Vol. 10 (1), 116-132
- https://doi.org/10.3390/ijms10010116
Abstract
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.This publication has 41 references indexed in Scilit:
- The microRNA regulated SBP-box genes SPL9 and SPL15 control shoot maturation in ArabidopsisPlant Molecular Biology, 2008
- Genomic Survey and Gene Expression Analysis of the Basic Leucine Zipper Transcription Factor Family in RicePlant Physiology, 2007
- AtPID: Arabidopsis thaliana protein interactome database an integrative platform for plant systems biologyNucleic Acids Research, 2007
- MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stressBMC Genomics, 2007
- F-Box Proteins in Rice. Genome-Wide Analysis, Classification, Temporal and Spatial Gene Expression during Panicle and Seed Development, and Regulation by Light and Abiotic StressPlant Physiology, 2007
- GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloringBioinformatics, 2006
- NCBI GEO: mining tens of millions of expression profiles--database and tools updateNucleic Acids Research, 2006
- Transcriptional Coordination of the Metabolic Network in ArabidopsisPlant Physiology, 2006
- BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological NetworksBioinformatics, 2005
- A gene expression map of Arabidopsis thaliana developmentNature Genetics, 2005