Using scale and feather traits for module construction provides a functional approach to chicken epidermal development
Gene co-expression network analysis has been a research method widely used in systematically exploring gene function and interaction. Using the Weighted Gene Co-expression Network Analysis (WGCNA) approach to construct a gene co-expression network using data from a customized 44K microarray transcri...
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| Published in | Functional & integrative genomics Vol. 17; no. 6; pp. 641 - 651 |
|---|---|
| Main Authors | , , |
| Format | Journal Article |
| Language | English |
| Published |
Berlin/Heidelberg
Springer Berlin Heidelberg
01.11.2017
Springer Nature B.V |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1438-793X 1438-7948 1438-7948 |
| DOI | 10.1007/s10142-017-0561-0 |
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| Abstract | Gene co-expression network analysis has been a research method widely used in systematically exploring gene function and interaction. Using the Weighted Gene Co-expression Network Analysis (WGCNA) approach to construct a gene co-expression network using data from a customized 44K microarray transcriptome of chicken epidermal embryogenesis, we have identified two distinct modules that are highly correlated with scale or feather development traits. Signaling pathways related to feather development were enriched in the traditional KEGG pathway analysis and functional terms relating specifically to embryonic epidermal development were also enriched in the Gene Ontology analysis. Significant enrichment annotations were discovered from customized enrichment tools such as Modular Single-Set Enrichment Test (MSET) and Medical Subject Headings (MeSH). Hub genes in both trait-correlated modules showed strong specific functional enrichment toward epidermal development. Also, regulatory elements, such as transcription factors and miRNAs, were targeted in the significant enrichment result. This work highlights the advantage of this methodology for functional prediction of genes not previously associated with scale- and feather trait-related modules. |
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| AbstractList | Gene co-expression network analysis has been a research method widely used in systematically exploring gene function and interaction. Using the Weighted Gene Co-expression Network Analysis (WGCNA) approach to construct a gene co-expression network using data from a customized 44K microarray transcriptome of chicken epidermal embryogenesis, we have identified two distinct modules that are highly correlated with scale or feather development traits. Signaling pathways related to feather development were enriched in the traditional KEGG pathway analysis and functional terms relating specifically to embryonic epidermal development were also enriched in the Gene Ontology analysis. Significant enrichment annotations were discovered from customized enrichment tools such as Modular Single-Set Enrichment Test (MSET) and Medical Subject Headings (MeSH). Hub genes in both trait-correlated modules showed strong specific functional enrichment toward epidermal development. Also, regulatory elements, such as transcription factors and miRNAs, were targeted in the significant enrichment result. This work highlights the advantage of this methodology for functional prediction of genes not previously associated with scale- and feather trait-related modules. Gene co-expression network analysis has been a research method widely used in systematically exploring gene function and interaction. Using the Weighted Gene Co-expression Network Analysis (WGCNA) approach to construct a gene co-expression network using data from a customized 44K microarray transcriptome of chicken epidermal embryogenesis, we have identified two distinct modules that are highly correlated with scale or feather development traits. Signaling pathways related to feather development were enriched in the traditional KEGG pathway analysis and functional terms relating specifically to embryonic epidermal development were also enriched in the Gene Ontology analysis. Significant enrichment annotations were discovered from customized enrichment tools such as Modular Single-Set Enrichment Test (MSET) and Medical Subject Headings (MeSH). Hub genes in both trait-correlated modules showed strong specific functional enrichment toward epidermal development. Also, regulatory elements, such as transcription factors and miRNAs, were targeted in the significant enrichment result. This work highlights the advantage of this methodology for functional prediction of genes not previously associated with scale- and feather trait-related modules.Gene co-expression network analysis has been a research method widely used in systematically exploring gene function and interaction. Using the Weighted Gene Co-expression Network Analysis (WGCNA) approach to construct a gene co-expression network using data from a customized 44K microarray transcriptome of chicken epidermal embryogenesis, we have identified two distinct modules that are highly correlated with scale or feather development traits. Signaling pathways related to feather development were enriched in the traditional KEGG pathway analysis and functional terms relating specifically to embryonic epidermal development were also enriched in the Gene Ontology analysis. Significant enrichment annotations were discovered from customized enrichment tools such as Modular Single-Set Enrichment Test (MSET) and Medical Subject Headings (MeSH). Hub genes in both trait-correlated modules showed strong specific functional enrichment toward epidermal development. Also, regulatory elements, such as transcription factors and miRNAs, were targeted in the significant enrichment result. This work highlights the advantage of this methodology for functional prediction of genes not previously associated with scale- and feather trait-related modules. |
| Author | Bao, Weier Greenwold, Matthew J. Sawyer, Roger H. |
| Author_xml | – sequence: 1 givenname: Weier orcidid: 0000-0001-5166-1501 surname: Bao fullname: Bao, Weier email: bao2@email.sc.edu organization: Department of Biological Sciences, University of South Carolina – sequence: 2 givenname: Matthew J. surname: Greenwold fullname: Greenwold, Matthew J. organization: Department of Biological Sciences, University of South Carolina – sequence: 3 givenname: Roger H. surname: Sawyer fullname: Sawyer, Roger H. organization: Department of Biological Sciences, University of South Carolina |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/28477104$$D View this record in MEDLINE/PubMed |
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| CitedBy_id | crossref_primary_10_1139_gen_2020_0054 crossref_primary_10_1007_s10142_018_0607_y |
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| Keywords | Epidermal development Enrichment analysis Microarray Co-expression network |
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| SubjectTerms | Animal Genetics and Genomics Animal Scales - growth & development Animal Scales - metabolism Animals Avian Proteins - genetics Avian Proteins - metabolism Biochemistry Bioinformatics Biomedical and Life Sciences Cell Biology chickens Chickens - genetics DNA microarrays Embryogenesis Epidermis - growth & development Epidermis - metabolism feathers Feathers - growth & development Feathers - metabolism Gene expression gene ontology Genes Life Sciences Medical Subject Headings-MeSH microarray technology Microbial Genetics and Genomics microRNA Original Article Plant Genetics and Genomics Poultry prediction Quantitative Trait, Heritable Regulatory sequences signal transduction transcription (genetics) Transcription factors Transcription Factors - genetics Transcription Factors - metabolism Transcriptome |
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| Title | Using scale and feather traits for module construction provides a functional approach to chicken epidermal development |
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