PsyMuKB: An Integrative De Novo Variant Knowledge Base for Developmental Disorders
De novo variants (DNVs) are one of the most significant contributors to severe early-onset genetic disorders such as autism spectrum disorder, intellectual disability, and other developmental and neuropsychiatric (DNP) disorders. Presently, a plethora of DNVs have been identified using next-generati...
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2019-08-01
|
| Series: | Genomics, Proteomics & Bioinformatics |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1672022919301585 |
| _version_ | 1797369631404457984 |
|---|---|
| author | Guan Ning Lin Sijia Guo Xian Tan Weidi Wang Wei Qian Weichen Song Jingru Wang Shunying Yu Zhen Wang Donghong Cui Han Wang |
| author_facet | Guan Ning Lin Sijia Guo Xian Tan Weidi Wang Wei Qian Weichen Song Jingru Wang Shunying Yu Zhen Wang Donghong Cui Han Wang |
| author_sort | Guan Ning Lin |
| collection | DOAJ |
| description | De novo variants (DNVs) are one of the most significant contributors to severe early-onset genetic disorders such as autism spectrum disorder, intellectual disability, and other developmental and neuropsychiatric (DNP) disorders. Presently, a plethora of DNVs have been identified using next-generation sequencing, and many efforts have been made to understand their impact at the gene level. However, there has been little exploration of the effects at the isoform level. The brain contains a high level of alternative splicing and regulation, and exhibits a more divergent splicing program than other tissues. Therefore, it is crucial to explore variants at the transcriptional regulation level to better interpret the mechanisms underlying DNP disorders. To facilitate a better usage and improve the isoform-level interpretation of variants, we developed NeuroPsychiatric Mutation Knowledge Base (PsyMuKB). It contains a comprehensive, carefully curated list of DNVs with transcriptional and translational annotations to enable identification of isoform-specific mutations. PsyMuKB allows a flexible search of genes or variants and provides both table-based descriptions and associated visualizations, such as expression, transcript genomic structures, protein interactions, and the mutation sites mapped on the protein structures. It also provides an easy-to-use web interface, allowing users to rapidly visualize the locations and characteristics of mutations and the expression patterns of the impacted genes and isoforms. PsyMuKB thus constitutes a valuable resource for identifying tissue-specific DNVs for further functional studies of related disorders. PsyMuKB is freely accessible at http://psymukb.net. Keywords: De novo mutation, Developmental and neuropsychiatric disorders, Database, Isoforms, Tissue specificity |
| first_indexed | 2024-03-08T17:49:42Z |
| format | Article |
| id | doaj.art-04b8e8b237234f11b5ba73c459c20e9e |
| institution | Directory Open Access Journal |
| issn | 1672-0229 |
| language | English |
| last_indexed | 2024-03-08T17:49:42Z |
| publishDate | 2019-08-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Genomics, Proteomics & Bioinformatics |
| spelling | doaj.art-04b8e8b237234f11b5ba73c459c20e9e2024-01-02T08:36:11ZengElsevierGenomics, Proteomics & Bioinformatics1672-02292019-08-01174453464PsyMuKB: An Integrative De Novo Variant Knowledge Base for Developmental DisordersGuan Ning Lin0Sijia Guo1Xian Tan2Weidi Wang3Wei Qian4Weichen Song5Jingru Wang6Shunying Yu7Zhen Wang8Donghong Cui9Han Wang10Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai 200030, China; Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200030, China; Corresponding authors.College of Information Science and Technology, Northeast Normal University, Changchun 130117, China; Institution of Computational Biology, Northeast Normal University, Changchun 130117, ChinaCollege of Information Science and Technology, Northeast Normal University, Changchun 130117, China; Institution of Computational Biology, Northeast Normal University, Changchun 130117, ChinaShanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai 200030, ChinaShanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, ChinaShanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, ChinaCollege of Information Science and Technology, Northeast Normal University, Changchun 130117, China; Institution of Computational Biology, Northeast Normal University, Changchun 130117, ChinaShanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai 200030, ChinaShanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai 200030, ChinaShanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai 200030, China; Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai 200030, China; Corresponding authors.College of Information Science and Technology, Northeast Normal University, Changchun 130117, China; Institution of Computational Biology, Northeast Normal University, Changchun 130117, China; Corresponding authors.De novo variants (DNVs) are one of the most significant contributors to severe early-onset genetic disorders such as autism spectrum disorder, intellectual disability, and other developmental and neuropsychiatric (DNP) disorders. Presently, a plethora of DNVs have been identified using next-generation sequencing, and many efforts have been made to understand their impact at the gene level. However, there has been little exploration of the effects at the isoform level. The brain contains a high level of alternative splicing and regulation, and exhibits a more divergent splicing program than other tissues. Therefore, it is crucial to explore variants at the transcriptional regulation level to better interpret the mechanisms underlying DNP disorders. To facilitate a better usage and improve the isoform-level interpretation of variants, we developed NeuroPsychiatric Mutation Knowledge Base (PsyMuKB). It contains a comprehensive, carefully curated list of DNVs with transcriptional and translational annotations to enable identification of isoform-specific mutations. PsyMuKB allows a flexible search of genes or variants and provides both table-based descriptions and associated visualizations, such as expression, transcript genomic structures, protein interactions, and the mutation sites mapped on the protein structures. It also provides an easy-to-use web interface, allowing users to rapidly visualize the locations and characteristics of mutations and the expression patterns of the impacted genes and isoforms. PsyMuKB thus constitutes a valuable resource for identifying tissue-specific DNVs for further functional studies of related disorders. PsyMuKB is freely accessible at http://psymukb.net. Keywords: De novo mutation, Developmental and neuropsychiatric disorders, Database, Isoforms, Tissue specificityhttp://www.sciencedirect.com/science/article/pii/S1672022919301585 |
| spellingShingle | Guan Ning Lin Sijia Guo Xian Tan Weidi Wang Wei Qian Weichen Song Jingru Wang Shunying Yu Zhen Wang Donghong Cui Han Wang PsyMuKB: An Integrative De Novo Variant Knowledge Base for Developmental Disorders Genomics, Proteomics & Bioinformatics |
| title | PsyMuKB: An Integrative De Novo Variant Knowledge Base for Developmental Disorders |
| title_full | PsyMuKB: An Integrative De Novo Variant Knowledge Base for Developmental Disorders |
| title_fullStr | PsyMuKB: An Integrative De Novo Variant Knowledge Base for Developmental Disorders |
| title_full_unstemmed | PsyMuKB: An Integrative De Novo Variant Knowledge Base for Developmental Disorders |
| title_short | PsyMuKB: An Integrative De Novo Variant Knowledge Base for Developmental Disorders |
| title_sort | psymukb an integrative de novo variant knowledge base for developmental disorders |
| url | http://www.sciencedirect.com/science/article/pii/S1672022919301585 |
| work_keys_str_mv | AT guanninglin psymukbanintegrativedenovovariantknowledgebasefordevelopmentaldisorders AT sijiaguo psymukbanintegrativedenovovariantknowledgebasefordevelopmentaldisorders AT xiantan psymukbanintegrativedenovovariantknowledgebasefordevelopmentaldisorders AT weidiwang psymukbanintegrativedenovovariantknowledgebasefordevelopmentaldisorders AT weiqian psymukbanintegrativedenovovariantknowledgebasefordevelopmentaldisorders AT weichensong psymukbanintegrativedenovovariantknowledgebasefordevelopmentaldisorders AT jingruwang psymukbanintegrativedenovovariantknowledgebasefordevelopmentaldisorders AT shunyingyu psymukbanintegrativedenovovariantknowledgebasefordevelopmentaldisorders AT zhenwang psymukbanintegrativedenovovariantknowledgebasefordevelopmentaldisorders AT donghongcui psymukbanintegrativedenovovariantknowledgebasefordevelopmentaldisorders AT hanwang psymukbanintegrativedenovovariantknowledgebasefordevelopmentaldisorders |