Journal
BIOMOLECULES
Volume 8, Issue 3, Pages -Publisher
MDPI
DOI: 10.3390/biom8030070
Keywords
Caenorhabditis elegans; transcriptome; gene co-expression network; cuticle; hub gene
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Funding
- National Natural Science Foundation of China [81502091]
- Open Project of Key laboratory of Loquat Germplasm Innovation and Utilization, Putian University, Fujian Province [2017003]
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Caenorhabditis elegans (C. elegans) is a well-characterized metazoan, whose transcriptome has been profiled in different tissues, development stages, or other conditions. Large-scale transcriptomes can be reused for gene function annotation through systematic analysis of gene co-expression relationships. We collected 2101 microarray data from National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO), and identified 48 modules of co-expressed genes that correspond to tissues, development stages, and other experimental conditions. These modules provide an overview of the transcriptional organizations that may work under different conditions. By analyzing higher-order module networks, we found that nucleus and plasma membrane modules are more connected than other intracellular modules. Module-based gene function annotation may help to extend the candidate cuticle gene list. A comparison with other published data validates the credibility of our result. Our findings provide a new source for future gene discovery in C. elegans.
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