Functional Annotation of Caenorhabditis elegans Genes by Analysis of Gene Co-Expression Networks
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 relations...
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| Format: | Article |
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MDPI AG
2018-08-01
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| Series: | Biomolecules |
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| Online Access: | http://www.mdpi.com/2218-273X/8/3/70 |
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| author | Wei Liu Ling Li Yiruo He Sen Cai Wenjie Zhao Hao Zheng Yuexian Zhong Shaobo Wang Yang Zou Zhenhua Xu Yu Zhang Wei Tu |
| author_facet | Wei Liu Ling Li Yiruo He Sen Cai Wenjie Zhao Hao Zheng Yuexian Zhong Shaobo Wang Yang Zou Zhenhua Xu Yu Zhang Wei Tu |
| author_sort | Wei Liu |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-12T04:03:03Z |
| format | Article |
| id | doaj.art-7c7f4a20e5e54919983b7c2715062127 |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-12-12T04:03:03Z |
| publishDate | 2018-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-7c7f4a20e5e54919983b7c27150621272022-12-22T00:38:52ZengMDPI AGBiomolecules2218-273X2018-08-01837010.3390/biom8030070biom8030070Functional Annotation of Caenorhabditis elegans Genes by Analysis of Gene Co-Expression NetworksWei Liu0Ling Li1Yiruo He2Sen Cai3Wenjie Zhao4Hao Zheng5Yuexian Zhong6Shaobo Wang7Yang Zou8Zhenhua Xu9Yu Zhang10Wei Tu11School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaSchool of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaSchool of Science and Engineering, The Chinese University of Hong Kong, Shenzhen 518172, ChinaSchool of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaSchool of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaSchool of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaSchool of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaSchool of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaSchool of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaSchool of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaSchool of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, ChinaDepartment of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114, USACaenorhabditis 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.http://www.mdpi.com/2218-273X/8/3/70Caenorhabditis eleganstranscriptomegene co-expression networkcuticlehub gene |
| spellingShingle | Wei Liu Ling Li Yiruo He Sen Cai Wenjie Zhao Hao Zheng Yuexian Zhong Shaobo Wang Yang Zou Zhenhua Xu Yu Zhang Wei Tu Functional Annotation of Caenorhabditis elegans Genes by Analysis of Gene Co-Expression Networks Biomolecules Caenorhabditis elegans transcriptome gene co-expression network cuticle hub gene |
| title | Functional Annotation of Caenorhabditis elegans Genes by Analysis of Gene Co-Expression Networks |
| title_full | Functional Annotation of Caenorhabditis elegans Genes by Analysis of Gene Co-Expression Networks |
| title_fullStr | Functional Annotation of Caenorhabditis elegans Genes by Analysis of Gene Co-Expression Networks |
| title_full_unstemmed | Functional Annotation of Caenorhabditis elegans Genes by Analysis of Gene Co-Expression Networks |
| title_short | Functional Annotation of Caenorhabditis elegans Genes by Analysis of Gene Co-Expression Networks |
| title_sort | functional annotation of caenorhabditis elegans genes by analysis of gene co expression networks |
| topic | Caenorhabditis elegans transcriptome gene co-expression network cuticle hub gene |
| url | http://www.mdpi.com/2218-273X/8/3/70 |
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