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VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases

Integrated analysis of DNA variants and gene expression profiles may facilitate precise identification of gene regulatory networks involved in disease mechanisms. Despite the widespread availability of public resources, we lack databases that are capable of simultaneously providing gene expression p...

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Autores principales: Lee, Chien-Yueh, Chattopadhyay, Amrita, Chiang, Li-Mei, Juang, Jyh-Ming Jimmy, Lai, Liang-Chuan, Tsai, Mong-Hsun, Lu, Tzu-Pin, Chuang, Eric Y
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6637258/
https://www.ncbi.nlm.nih.gov/pubmed/31317185
http://dx.doi.org/10.1093/database/baz075
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author Lee, Chien-Yueh
Chattopadhyay, Amrita
Chiang, Li-Mei
Juang, Jyh-Ming Jimmy
Lai, Liang-Chuan
Tsai, Mong-Hsun
Lu, Tzu-Pin
Chuang, Eric Y
author_facet Lee, Chien-Yueh
Chattopadhyay, Amrita
Chiang, Li-Mei
Juang, Jyh-Ming Jimmy
Lai, Liang-Chuan
Tsai, Mong-Hsun
Lu, Tzu-Pin
Chuang, Eric Y
author_sort Lee, Chien-Yueh
collection PubMed
description Integrated analysis of DNA variants and gene expression profiles may facilitate precise identification of gene regulatory networks involved in disease mechanisms. Despite the widespread availability of public resources, we lack databases that are capable of simultaneously providing gene expression profiles, variant annotations, functional prediction scores and pathogenic analyses. VariED is the first web-based querying system that integrates an annotation database and expression profiles for genetic variants. The database offers a user-friendly platform and locates gene/variant names in the literature by connecting to established online querying tools, biological annotation tools and records from free-text literature. VariED acts as a central hub for organized genome information consisting of gene annotation, variant allele frequency, functional prediction, clinical interpretation and gene expression profiles in three species: human, mouse and zebrafish. VariED also provides a novel scoring scheme to predict the functional impact of a DNA variant. With one single entry, all results regarding queried DNA variants can be downloaded. VariED can potentially serve as an efficient way to obtain comprehensive variant knowledge for clinicians and scientists around the world working on important drug discoveries and precision treatments.
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spelling pubmed-66372582019-07-22 VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases Lee, Chien-Yueh Chattopadhyay, Amrita Chiang, Li-Mei Juang, Jyh-Ming Jimmy Lai, Liang-Chuan Tsai, Mong-Hsun Lu, Tzu-Pin Chuang, Eric Y Database (Oxford) Database Tool Integrated analysis of DNA variants and gene expression profiles may facilitate precise identification of gene regulatory networks involved in disease mechanisms. Despite the widespread availability of public resources, we lack databases that are capable of simultaneously providing gene expression profiles, variant annotations, functional prediction scores and pathogenic analyses. VariED is the first web-based querying system that integrates an annotation database and expression profiles for genetic variants. The database offers a user-friendly platform and locates gene/variant names in the literature by connecting to established online querying tools, biological annotation tools and records from free-text literature. VariED acts as a central hub for organized genome information consisting of gene annotation, variant allele frequency, functional prediction, clinical interpretation and gene expression profiles in three species: human, mouse and zebrafish. VariED also provides a novel scoring scheme to predict the functional impact of a DNA variant. With one single entry, all results regarding queried DNA variants can be downloaded. VariED can potentially serve as an efficient way to obtain comprehensive variant knowledge for clinicians and scientists around the world working on important drug discoveries and precision treatments. Oxford University Press 2019-07-17 /pmc/articles/PMC6637258/ /pubmed/31317185 http://dx.doi.org/10.1093/database/baz075 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Tool
Lee, Chien-Yueh
Chattopadhyay, Amrita
Chiang, Li-Mei
Juang, Jyh-Ming Jimmy
Lai, Liang-Chuan
Tsai, Mong-Hsun
Lu, Tzu-Pin
Chuang, Eric Y
VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases
title VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases
title_full VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases
title_fullStr VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases
title_full_unstemmed VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases
title_short VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases
title_sort varied: the first integrated database of gene annotation and expression profiles for variants related to human diseases
topic Database Tool
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6637258/
https://www.ncbi.nlm.nih.gov/pubmed/31317185
http://dx.doi.org/10.1093/database/baz075
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