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CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-related Genes and Clinical Manifestations
Congenital heart disease (CHD) is one of the most common causes of major birth defects, with a prevalence of 1%. Although an increasing number of studies have reported the etiology of CHD, the findings scattered throughout the literature are difficult to retrieve and utilize in research and clinical...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10372913/ https://www.ncbi.nlm.nih.gov/pubmed/35961607 http://dx.doi.org/10.1016/j.gpb.2022.08.001 |
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author | Zhou, Wei-Zhen Li, Wenke Shen, Huayan Wang, Ruby W. Chen, Wen Zhang, Yujing Zeng, Qingyi Wang, Hao Yuan, Meng Zeng, Ziyi Cui, Jinhui Li, Chuan-Yun Ye, Fred Y. Zhou, Zhou |
author_facet | Zhou, Wei-Zhen Li, Wenke Shen, Huayan Wang, Ruby W. Chen, Wen Zhang, Yujing Zeng, Qingyi Wang, Hao Yuan, Meng Zeng, Ziyi Cui, Jinhui Li, Chuan-Yun Ye, Fred Y. Zhou, Zhou |
author_sort | Zhou, Wei-Zhen |
collection | PubMed |
description | Congenital heart disease (CHD) is one of the most common causes of major birth defects, with a prevalence of 1%. Although an increasing number of studies have reported the etiology of CHD, the findings scattered throughout the literature are difficult to retrieve and utilize in research and clinical practice. We therefore developed CHDbase, an evidence-based knowledgebase of CHD-related genes and clinical manifestations manually curated from 1114 publications, linking 1124 susceptibility genes and 3591 variations to more than 300 CHD types and related syndromes. Metadata such as the information of each publication and the selected population and samples, the strategy of studies, and the major findings of studies were integrated with each item of the research record. We also integrated functional annotations through parsing ∼ 50 databases/tools to facilitate the interpretation of these genes and variations in disease pathogenicity. We further prioritized the significance of these CHD-related genes with a gene interaction network approach and extracted a core CHD sub-network with 163 genes. The clear genetic landscape of CHD enables the phenotype classification based on the shared genetic origin. Overall, CHDbase provides a comprehensive and freely available resource to study CHD susceptibilities, supporting a wide range of users in the scientific and medical communities. CHDbase is accessible at http://chddb.fwgenetics.org. |
format | Online Article Text |
id | pubmed-10372913 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-103729132023-07-28 CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-related Genes and Clinical Manifestations Zhou, Wei-Zhen Li, Wenke Shen, Huayan Wang, Ruby W. Chen, Wen Zhang, Yujing Zeng, Qingyi Wang, Hao Yuan, Meng Zeng, Ziyi Cui, Jinhui Li, Chuan-Yun Ye, Fred Y. Zhou, Zhou Genomics Proteomics Bioinformatics Database Congenital heart disease (CHD) is one of the most common causes of major birth defects, with a prevalence of 1%. Although an increasing number of studies have reported the etiology of CHD, the findings scattered throughout the literature are difficult to retrieve and utilize in research and clinical practice. We therefore developed CHDbase, an evidence-based knowledgebase of CHD-related genes and clinical manifestations manually curated from 1114 publications, linking 1124 susceptibility genes and 3591 variations to more than 300 CHD types and related syndromes. Metadata such as the information of each publication and the selected population and samples, the strategy of studies, and the major findings of studies were integrated with each item of the research record. We also integrated functional annotations through parsing ∼ 50 databases/tools to facilitate the interpretation of these genes and variations in disease pathogenicity. We further prioritized the significance of these CHD-related genes with a gene interaction network approach and extracted a core CHD sub-network with 163 genes. The clear genetic landscape of CHD enables the phenotype classification based on the shared genetic origin. Overall, CHDbase provides a comprehensive and freely available resource to study CHD susceptibilities, supporting a wide range of users in the scientific and medical communities. CHDbase is accessible at http://chddb.fwgenetics.org. Elsevier 2023-02 2022-08-10 /pmc/articles/PMC10372913/ /pubmed/35961607 http://dx.doi.org/10.1016/j.gpb.2022.08.001 Text en © 2023 The Authors https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Database Zhou, Wei-Zhen Li, Wenke Shen, Huayan Wang, Ruby W. Chen, Wen Zhang, Yujing Zeng, Qingyi Wang, Hao Yuan, Meng Zeng, Ziyi Cui, Jinhui Li, Chuan-Yun Ye, Fred Y. Zhou, Zhou CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-related Genes and Clinical Manifestations |
title | CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-related Genes and Clinical Manifestations |
title_full | CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-related Genes and Clinical Manifestations |
title_fullStr | CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-related Genes and Clinical Manifestations |
title_full_unstemmed | CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-related Genes and Clinical Manifestations |
title_short | CHDbase: A Comprehensive Knowledgebase for Congenital Heart Disease-related Genes and Clinical Manifestations |
title_sort | chdbase: a comprehensive knowledgebase for congenital heart disease-related genes and clinical manifestations |
topic | Database |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10372913/ https://www.ncbi.nlm.nih.gov/pubmed/35961607 http://dx.doi.org/10.1016/j.gpb.2022.08.001 |
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