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Functional Annotation of Caenorhabditis elegans Genes by Analysis of Gene Co-Expression Networks.


ABSTRACT: 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.

SUBMITTER: Liu W 

PROVIDER: S-EPMC6163173 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

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Functional Annotation of <i>Caenorhabditis elegans</i> Genes by Analysis of Gene Co-Expression Networks.

Liu Wei W   Li Ling L   He Yiruo Y   Cai Sen S   Zhao Wenjie W   Zheng Hao H   Zhong Yuexian Y   Wang Shaobo S   Zou Yang Y   Xu Zhenhua Z   Zhang Yu Y   Tu Wei W  

Biomolecules 20180803 3


<i>Caenorhabditis elegans</i> (<i>C. elegans</i>) 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 corres  ...[more]

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