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Using WGCNA (weighted gene co-expression network analysis) to identify the hub genes of skin hair follicle development in fetus stage of Inner Mongolia cashmere goat
OBJECTIVE: Mature hair follicles represent an important stage of hair follicle development, which determines the stability of hair follicle structure and its ability to enter the hair cycle. Here, we used weighted gene co-expression network analysis (WGCNA) to identify hub genes of mature skin and h...
Autores principales: | , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7755285/ https://www.ncbi.nlm.nih.gov/pubmed/33351808 http://dx.doi.org/10.1371/journal.pone.0243507 |
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author | Wu, Zhihong Hai, Erhan Di, Zhengyang Ma, Rong Shang, Fangzheng Wang, Yu Wang, Min Liang, Lili Rong, Youjun Pan, Jianfeng Wu, Wenbin Su, Rui Wang, Zhiying Wang, Ruijun Zhang, Yanjun Li, Jinquan |
author_facet | Wu, Zhihong Hai, Erhan Di, Zhengyang Ma, Rong Shang, Fangzheng Wang, Yu Wang, Min Liang, Lili Rong, Youjun Pan, Jianfeng Wu, Wenbin Su, Rui Wang, Zhiying Wang, Ruijun Zhang, Yanjun Li, Jinquan |
author_sort | Wu, Zhihong |
collection | PubMed |
description | OBJECTIVE: Mature hair follicles represent an important stage of hair follicle development, which determines the stability of hair follicle structure and its ability to enter the hair cycle. Here, we used weighted gene co-expression network analysis (WGCNA) to identify hub genes of mature skin and hair follicles in Inner Mongolian cashmere goats. METHODS: We used transcriptome sequencing data for the skin of Inner Mongolian cashmere goats from fetal days 45–135 days, and divided the co expressed genes into different modules by WGCNA. Characteristic values were used to screen out modules that were highly expressed in mature skin follicles. Module hub genes were then selected based on the correlation coefficients between the gene and module eigenvalue, gene connectivity, and Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The results were confirmed by quantitative polymerase chain reaction (qPCR). RESULTS: Ten modules were successfully defined, of which one, with a total of 3166 genes, was selected as a specific module through sample and gene expression pattern analyses. A total of 584 candidate hub genes in the module were screened by the correlation coefficients between the genes and module eigenvalue and gene connectivity. Finally, GO/KEGG functional enrichment analyses detected WNT10A as a key gene in the development and maturation of skin hair follicles in fetal Inner Mongolian cashmere goats. qPCR showed that the expression trends of 13 genes from seven fetal skin samples were consistent with the sequencing results, indicating that the sequencing results were reliable.n |
format | Online Article Text |
id | pubmed-7755285 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-77552852021-01-06 Using WGCNA (weighted gene co-expression network analysis) to identify the hub genes of skin hair follicle development in fetus stage of Inner Mongolia cashmere goat Wu, Zhihong Hai, Erhan Di, Zhengyang Ma, Rong Shang, Fangzheng Wang, Yu Wang, Min Liang, Lili Rong, Youjun Pan, Jianfeng Wu, Wenbin Su, Rui Wang, Zhiying Wang, Ruijun Zhang, Yanjun Li, Jinquan PLoS One Research Article OBJECTIVE: Mature hair follicles represent an important stage of hair follicle development, which determines the stability of hair follicle structure and its ability to enter the hair cycle. Here, we used weighted gene co-expression network analysis (WGCNA) to identify hub genes of mature skin and hair follicles in Inner Mongolian cashmere goats. METHODS: We used transcriptome sequencing data for the skin of Inner Mongolian cashmere goats from fetal days 45–135 days, and divided the co expressed genes into different modules by WGCNA. Characteristic values were used to screen out modules that were highly expressed in mature skin follicles. Module hub genes were then selected based on the correlation coefficients between the gene and module eigenvalue, gene connectivity, and Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The results were confirmed by quantitative polymerase chain reaction (qPCR). RESULTS: Ten modules were successfully defined, of which one, with a total of 3166 genes, was selected as a specific module through sample and gene expression pattern analyses. A total of 584 candidate hub genes in the module were screened by the correlation coefficients between the genes and module eigenvalue and gene connectivity. Finally, GO/KEGG functional enrichment analyses detected WNT10A as a key gene in the development and maturation of skin hair follicles in fetal Inner Mongolian cashmere goats. qPCR showed that the expression trends of 13 genes from seven fetal skin samples were consistent with the sequencing results, indicating that the sequencing results were reliable.n Public Library of Science 2020-12-22 /pmc/articles/PMC7755285/ /pubmed/33351808 http://dx.doi.org/10.1371/journal.pone.0243507 Text en © 2020 Wu et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Wu, Zhihong Hai, Erhan Di, Zhengyang Ma, Rong Shang, Fangzheng Wang, Yu Wang, Min Liang, Lili Rong, Youjun Pan, Jianfeng Wu, Wenbin Su, Rui Wang, Zhiying Wang, Ruijun Zhang, Yanjun Li, Jinquan Using WGCNA (weighted gene co-expression network analysis) to identify the hub genes of skin hair follicle development in fetus stage of Inner Mongolia cashmere goat |
title | Using WGCNA (weighted gene co-expression network analysis) to identify the hub genes of skin hair follicle development in fetus stage of Inner Mongolia cashmere goat |
title_full | Using WGCNA (weighted gene co-expression network analysis) to identify the hub genes of skin hair follicle development in fetus stage of Inner Mongolia cashmere goat |
title_fullStr | Using WGCNA (weighted gene co-expression network analysis) to identify the hub genes of skin hair follicle development in fetus stage of Inner Mongolia cashmere goat |
title_full_unstemmed | Using WGCNA (weighted gene co-expression network analysis) to identify the hub genes of skin hair follicle development in fetus stage of Inner Mongolia cashmere goat |
title_short | Using WGCNA (weighted gene co-expression network analysis) to identify the hub genes of skin hair follicle development in fetus stage of Inner Mongolia cashmere goat |
title_sort | using wgcna (weighted gene co-expression network analysis) to identify the hub genes of skin hair follicle development in fetus stage of inner mongolia cashmere goat |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7755285/ https://www.ncbi.nlm.nih.gov/pubmed/33351808 http://dx.doi.org/10.1371/journal.pone.0243507 |
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