Weighted Gene Co-Expression Network Analysis (WGCNA) Discovered Novel Long Non-Coding RNAs for Polycystic Ovary Syndrome
Polycystic ovary syndrome (PCOS) affects reproductive-age women. This condition causes infertility, insulin resistance, obesity, and heart difficulties. The molecular basis and mechanism of PCOS might potentially generate effective treatments. Long non-coding RNAs (lncRNAs) show control over multifa...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-02-01
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| Series: | Biomedicines |
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| Online Access: | https://www.mdpi.com/2227-9059/11/2/518 |
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| author | Roozbeh Heidarzadehpilehrood Maryam Pirhoushiaran Malina Binti Osman Habibah Abdul Hamid King-Hwa Ling |
| author_facet | Roozbeh Heidarzadehpilehrood Maryam Pirhoushiaran Malina Binti Osman Habibah Abdul Hamid King-Hwa Ling |
| author_sort | Roozbeh Heidarzadehpilehrood |
| collection | DOAJ |
| description | Polycystic ovary syndrome (PCOS) affects reproductive-age women. This condition causes infertility, insulin resistance, obesity, and heart difficulties. The molecular basis and mechanism of PCOS might potentially generate effective treatments. Long non-coding RNAs (lncRNAs) show control over multifactorial disorders’ growth and incidence. Numerous studies have emphasized its significance and alterations in PCOS. We used bioinformatic methods to find novel dysregulated lncRNAs in PCOS. To achieve this objective, the gene expression profile of GSE48301, comprising PCOS patients and normal control tissue samples, was evaluated using the R limma package with the following cut-off criterion: <i>p</i>-value < 0.05. Firstly, weighted gene co-expression network analysis (WGCNA) was used to determine the co-expression genes of lncRNAs; subsequently, hub gene identification and pathway enrichment analysis were used. With the defined criteria, nine novel dysregulated lncRNAs were identified. In WGCNA, different colors represent different modules. In the current study, WGCNA resulted in turquoise, gray, blue, and black co-expression modules with dysregulated lncRNAs. The pathway enrichment analysis of these co-expressed modules revealed enrichment in PCOS-associated pathways, including gene expression, signal transduction, metabolism, and apoptosis. In addition, <i>CCT7</i>, <i>EFTUD2</i>, <i>ESR1</i>, <i>JUN</i>, <i>NDUFAB1</i>, <i>CTTNB1</i>, <i>GRB2</i>, and <i>CTNNB1</i> were identified as hub genes, and some of them have been investigated in PCOS. This study uncovered nine novel PCOS-related lncRNAs. To confirm how these lncRNAs control translational modification in PCOS, functional studies are required. |
| first_indexed | 2024-03-11T09:07:00Z |
| format | Article |
| id | doaj.art-782cddf8e6c946ff811b9c96908a962d |
| institution | Directory Open Access Journal |
| issn | 2227-9059 |
| language | English |
| last_indexed | 2024-03-11T09:07:00Z |
| publishDate | 2023-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomedicines |
| spelling | doaj.art-782cddf8e6c946ff811b9c96908a962d2023-11-16T19:19:24ZengMDPI AGBiomedicines2227-90592023-02-0111251810.3390/biomedicines11020518Weighted Gene Co-Expression Network Analysis (WGCNA) Discovered Novel Long Non-Coding RNAs for Polycystic Ovary SyndromeRoozbeh Heidarzadehpilehrood0Maryam Pirhoushiaran1Malina Binti Osman2Habibah Abdul Hamid3King-Hwa Ling4Department of Obstetrics & Gynaecology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, MalaysiaDepartment of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran 1417613151, IranDepartment of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, MalaysiaDepartment of Obstetrics & Gynaecology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, MalaysiaDepartment of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, MalaysiaPolycystic ovary syndrome (PCOS) affects reproductive-age women. This condition causes infertility, insulin resistance, obesity, and heart difficulties. The molecular basis and mechanism of PCOS might potentially generate effective treatments. Long non-coding RNAs (lncRNAs) show control over multifactorial disorders’ growth and incidence. Numerous studies have emphasized its significance and alterations in PCOS. We used bioinformatic methods to find novel dysregulated lncRNAs in PCOS. To achieve this objective, the gene expression profile of GSE48301, comprising PCOS patients and normal control tissue samples, was evaluated using the R limma package with the following cut-off criterion: <i>p</i>-value < 0.05. Firstly, weighted gene co-expression network analysis (WGCNA) was used to determine the co-expression genes of lncRNAs; subsequently, hub gene identification and pathway enrichment analysis were used. With the defined criteria, nine novel dysregulated lncRNAs were identified. In WGCNA, different colors represent different modules. In the current study, WGCNA resulted in turquoise, gray, blue, and black co-expression modules with dysregulated lncRNAs. The pathway enrichment analysis of these co-expressed modules revealed enrichment in PCOS-associated pathways, including gene expression, signal transduction, metabolism, and apoptosis. In addition, <i>CCT7</i>, <i>EFTUD2</i>, <i>ESR1</i>, <i>JUN</i>, <i>NDUFAB1</i>, <i>CTTNB1</i>, <i>GRB2</i>, and <i>CTNNB1</i> were identified as hub genes, and some of them have been investigated in PCOS. This study uncovered nine novel PCOS-related lncRNAs. To confirm how these lncRNAs control translational modification in PCOS, functional studies are required.https://www.mdpi.com/2227-9059/11/2/518PCOSlncRNAbioinformaticsWGCNAmodulehub gene |
| spellingShingle | Roozbeh Heidarzadehpilehrood Maryam Pirhoushiaran Malina Binti Osman Habibah Abdul Hamid King-Hwa Ling Weighted Gene Co-Expression Network Analysis (WGCNA) Discovered Novel Long Non-Coding RNAs for Polycystic Ovary Syndrome Biomedicines PCOS lncRNA bioinformatics WGCNA module hub gene |
| title | Weighted Gene Co-Expression Network Analysis (WGCNA) Discovered Novel Long Non-Coding RNAs for Polycystic Ovary Syndrome |
| title_full | Weighted Gene Co-Expression Network Analysis (WGCNA) Discovered Novel Long Non-Coding RNAs for Polycystic Ovary Syndrome |
| title_fullStr | Weighted Gene Co-Expression Network Analysis (WGCNA) Discovered Novel Long Non-Coding RNAs for Polycystic Ovary Syndrome |
| title_full_unstemmed | Weighted Gene Co-Expression Network Analysis (WGCNA) Discovered Novel Long Non-Coding RNAs for Polycystic Ovary Syndrome |
| title_short | Weighted Gene Co-Expression Network Analysis (WGCNA) Discovered Novel Long Non-Coding RNAs for Polycystic Ovary Syndrome |
| title_sort | weighted gene co expression network analysis wgcna discovered novel long non coding rnas for polycystic ovary syndrome |
| topic | PCOS lncRNA bioinformatics WGCNA module hub gene |
| url | https://www.mdpi.com/2227-9059/11/2/518 |
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