Functional Annotation of Caenorhabditis elegans Genes by Analysis of Gene Co-Expression Networks
AbstractCaenorhabditis 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. View Full-Text
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Liu, W.; Li, L.; He, Y.; Cai, S.; Zhao, W.; Zheng, H.; Zhong, Y.; Wang, S.; Zou, Y.; Xu, Z.; Zhang, Y.; Tu, W. Functional Annotation of Caenorhabditis elegans Genes by Analysis of Gene Co-Expression Networks. Biomolecules 2018, 8, 70.
Liu W, Li L, He Y, Cai S, Zhao W, Zheng H, Zhong Y, Wang S, Zou Y, Xu Z, Zhang Y, Tu W. Functional Annotation of Caenorhabditis elegans Genes by Analysis of Gene Co-Expression Networks. Biomolecules. 2018; 8(3):70.Chicago/Turabian Style
Liu, Wei; Li, Ling; He, Yiruo; Cai, Sen; Zhao, Wenjie; Zheng, Hao; Zhong, Yuexian; Wang, Shaobo; Zou, Yang; Xu, Zhenhua; Zhang, Yu; Tu, Wei. 2018. "Functional Annotation of Caenorhabditis elegans Genes by Analysis of Gene Co-Expression Networks." Biomolecules 8, no. 3: 70.
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