m6A-TSHub: Unveiling the Context-specific m6A Methylation and m6A-affecting Mutations in 23 Human Tissues
As the most pervasive epigenetic marker present on mRNAs and long non-coding RNAs (lncRNAs), N6-methyladenosine (m6A) RNA methylation has been shown to participate in essential biological processes. Recent studies have revealed the distinct patterns of m6A methylome across human tissues, and a major...
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| Format: | Article |
| Language: | English |
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Oxford University Press
2023-08-01
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| Series: | Genomics, Proteomics & Bioinformatics |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1672022922001140 |
| _version_ | 1827158559063801856 |
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| author | Bowen Song Daiyun Huang Yuxin Zhang Zhen Wei Jionglong Su João Pedro de Magalhães Daniel J. Rigden Jia Meng Kunqi Chen |
| author_facet | Bowen Song Daiyun Huang Yuxin Zhang Zhen Wei Jionglong Su João Pedro de Magalhães Daniel J. Rigden Jia Meng Kunqi Chen |
| author_sort | Bowen Song |
| collection | DOAJ |
| description | As the most pervasive epigenetic marker present on mRNAs and long non-coding RNAs (lncRNAs), N6-methyladenosine (m6A) RNA methylation has been shown to participate in essential biological processes. Recent studies have revealed the distinct patterns of m6A methylome across human tissues, and a major challenge remains in elucidating the tissue-specific presence and circuitry of m6A methylation. We present here a comprehensive online platform, m6A-TSHub, for unveiling the context-specific m6A methylation and genetic mutations that potentially regulate m6A epigenetic mark. m6A-TSHub consists of four core components, including (1) m6A-TSDB, a comprehensive database of 184,554 functionally annotated m6A sites derived from 23 human tissues and 499,369 m6A sites from 25 tumor conditions, respectively; (2) m6A-TSFinder, a web server for high-accuracy prediction of m6A methylation sites within a specific tissue from RNA sequences, which was constructed using multi-instance deep neural networks with gated attention; (3) m6A-TSVar, a web server for assessing the impact of genetic variants on tissue-specific m6A RNA modifications; and (4) m6A-CAVar, a database of 587,983 The Cancer Genome Atlas (TCGA) cancer mutations (derived from 27 cancer types) that were predicted to affect m6A modifications in the primary tissue of cancers. The database should make a useful resource for studying the m6A methylome and the genetic factors of epitranscriptome disturbance in a specific tissue (or cancer type). m6A-TSHub is accessible at www.xjtlu.edu.cn/biologicalsciences/m6ats. |
| first_indexed | 2024-03-08T18:30:44Z |
| format | Article |
| id | doaj.art-64edc163a5604d168eefcf22d58a8d11 |
| institution | Directory Open Access Journal |
| issn | 1672-0229 |
| language | English |
| last_indexed | 2025-03-20T23:43:09Z |
| publishDate | 2023-08-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | Genomics, Proteomics & Bioinformatics |
| spelling | doaj.art-64edc163a5604d168eefcf22d58a8d112024-08-03T12:54:35ZengOxford University PressGenomics, Proteomics & Bioinformatics1672-02292023-08-01214678694m6A-TSHub: Unveiling the Context-specific m6A Methylation and m6A-affecting Mutations in 23 Human TissuesBowen Song0Daiyun Huang1Yuxin Zhang2Zhen Wei3Jionglong Su4João Pedro de Magalhães5Daniel J. Rigden6Jia Meng7Kunqi Chen8Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350004, China; Department of Mathematical Sciences, Xi’an Jiaotong-Liverpool University, Suzhou 215123, China; Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United KingdomDepartment of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou 215123, China; Department of Computer Science, University of Liverpool, Liverpool L69 7ZB, United Kingdom; Corresponding authors.Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou 215123, ChinaDepartment of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou 215123, China; Institute of Ageing & Chronic Disease, University of Liverpool, Liverpool L69 7ZB, United KingdomSchool of AI and Advanced Computing, Xi’an Jiaotong-Liverpool University, Suzhou 215123, ChinaInstitute of Ageing & Chronic Disease, University of Liverpool, Liverpool L69 7ZB, United KingdomInstitute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United KingdomInstitute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom; Department of Biological Sciences, Xi’an Jiaotong-Liverpool University, Suzhou 215123, China; AI University Research Centre, Xi’an Jiaotong-Liverpool University, Suzhou 215123, ChinaKey Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350004, China; Corresponding authors.As the most pervasive epigenetic marker present on mRNAs and long non-coding RNAs (lncRNAs), N6-methyladenosine (m6A) RNA methylation has been shown to participate in essential biological processes. Recent studies have revealed the distinct patterns of m6A methylome across human tissues, and a major challenge remains in elucidating the tissue-specific presence and circuitry of m6A methylation. We present here a comprehensive online platform, m6A-TSHub, for unveiling the context-specific m6A methylation and genetic mutations that potentially regulate m6A epigenetic mark. m6A-TSHub consists of four core components, including (1) m6A-TSDB, a comprehensive database of 184,554 functionally annotated m6A sites derived from 23 human tissues and 499,369 m6A sites from 25 tumor conditions, respectively; (2) m6A-TSFinder, a web server for high-accuracy prediction of m6A methylation sites within a specific tissue from RNA sequences, which was constructed using multi-instance deep neural networks with gated attention; (3) m6A-TSVar, a web server for assessing the impact of genetic variants on tissue-specific m6A RNA modifications; and (4) m6A-CAVar, a database of 587,983 The Cancer Genome Atlas (TCGA) cancer mutations (derived from 27 cancer types) that were predicted to affect m6A modifications in the primary tissue of cancers. The database should make a useful resource for studying the m6A methylome and the genetic factors of epitranscriptome disturbance in a specific tissue (or cancer type). m6A-TSHub is accessible at www.xjtlu.edu.cn/biologicalsciences/m6ats.http://www.sciencedirect.com/science/article/pii/S1672022922001140N6-methyladenosineContext-specific analysisCancer mutationGenome analysisFunctional annotation |
| spellingShingle | Bowen Song Daiyun Huang Yuxin Zhang Zhen Wei Jionglong Su João Pedro de Magalhães Daniel J. Rigden Jia Meng Kunqi Chen m6A-TSHub: Unveiling the Context-specific m6A Methylation and m6A-affecting Mutations in 23 Human Tissues Genomics, Proteomics & Bioinformatics N6-methyladenosine Context-specific analysis Cancer mutation Genome analysis Functional annotation |
| title | m6A-TSHub: Unveiling the Context-specific m6A Methylation and m6A-affecting Mutations in 23 Human Tissues |
| title_full | m6A-TSHub: Unveiling the Context-specific m6A Methylation and m6A-affecting Mutations in 23 Human Tissues |
| title_fullStr | m6A-TSHub: Unveiling the Context-specific m6A Methylation and m6A-affecting Mutations in 23 Human Tissues |
| title_full_unstemmed | m6A-TSHub: Unveiling the Context-specific m6A Methylation and m6A-affecting Mutations in 23 Human Tissues |
| title_short | m6A-TSHub: Unveiling the Context-specific m6A Methylation and m6A-affecting Mutations in 23 Human Tissues |
| title_sort | m6a tshub unveiling the context specific m6a methylation and m6a affecting mutations in 23 human tissues |
| topic | N6-methyladenosine Context-specific analysis Cancer mutation Genome analysis Functional annotation |
| url | http://www.sciencedirect.com/science/article/pii/S1672022922001140 |
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