期刊
PLANTA
卷 249, 期 5, 页码 1487-1501出版社
SPRINGER
DOI: 10.1007/s00425-019-03102-9
关键词
Rice; Conservation; Hub gene; Transcriptome
资金
- National Natural Science Foundation of China [31270454, 81502091]
- Open Project of Key laboratory of Loquat Germplasm Innovation and Utilization, Putian University, Fujian Province [2017003]
Main conclusion A comprehensive network of the Arabidopsis transcriptome was analyzed and may serve as a valuable resource for candidate gene function investigations. A web tool to explore module information was also provided. Arabidopsis thaliana is a widely studied model plant whose transcriptome has been substantially profiled in various tissues, development stages and other conditions. These data can be reused for research on gene function through a systematic analysis of gene co-expression relationships. We collected microarray data from National Center for Biotechnology Information Gene Expression Omnibus, identified modules of co-expressed genes and annotated module functions. These modules were associated with experiments/traits, which provided potential signature modules for phenotypes. Novel heat shock proteins were implicated according to guilt by association. A higher-order module networks analysis suggested that the Arabidopsis network can be further organized into 15 meta-modules and that a chloroplast meta-module has a distinct gene expression pattern from the other 14 meta-modules. A comparison with the rice transcriptome revealed preserved modules and KEGG pathways. All the module gene information was available from an online tool at http://bioinformatics.fafu.edu.cniarabi/. Our findings provide a new source for future gene discovery in Arabidopsis.
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