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.
<h4>Objective</h4>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 o...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2020-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0243507 |
| _version_ | 1819035310036615168 |
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| author | Zhihong Wu Erhan Hai Zhengyang Di Rong Ma Fangzheng Shang Yu Wang Min Wang Lili Liang Youjun Rong Jianfeng Pan Wenbin Wu Rui Su Zhiying Wang Ruijun Wang Yanjun Zhang Jinquan Li |
| author_facet | Zhihong Wu Erhan Hai Zhengyang Di Rong Ma Fangzheng Shang Yu Wang Min Wang Lili Liang Youjun Rong Jianfeng Pan Wenbin Wu Rui Su Zhiying Wang Ruijun Wang Yanjun Zhang Jinquan Li |
| author_sort | Zhihong Wu |
| collection | DOAJ |
| description | <h4>Objective</h4>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.<h4>Methods</h4>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).<h4>Results</h4>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. |
| first_indexed | 2024-12-21T07:47:35Z |
| format | Article |
| id | doaj.art-3d9faf5f08b14b18a7ff370a82beda05 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-21T07:47:35Z |
| publishDate | 2020-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-3d9faf5f08b14b18a7ff370a82beda052022-12-21T19:11:09ZengPublic Library of Science (PLoS)PLoS ONE1932-62032020-01-011512e024350710.1371/journal.pone.0243507Using 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.Zhihong WuErhan HaiZhengyang DiRong MaFangzheng ShangYu WangMin WangLili LiangYoujun RongJianfeng PanWenbin WuRui SuZhiying WangRuijun WangYanjun ZhangJinquan Li<h4>Objective</h4>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.<h4>Methods</h4>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).<h4>Results</h4>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.https://doi.org/10.1371/journal.pone.0243507 |
| spellingShingle | Zhihong Wu Erhan Hai Zhengyang Di Rong Ma Fangzheng Shang Yu Wang Min Wang Lili Liang Youjun Rong Jianfeng Pan Wenbin Wu Rui Su Zhiying Wang Ruijun Wang Yanjun Zhang Jinquan Li 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. PLoS ONE |
| 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 |
| url | https://doi.org/10.1371/journal.pone.0243507 |
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