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VIRdb: a comprehensive database for interactive analysis of genes/proteins involved in the pathogenesis of vitiligo

Vitiligo is a chronic asymptomatic disorder affecting melanocytes from the basal layer of the epidermis which leads to a patchy loss of skin color. Even though it is one of the neglected disease conditions, people suffering from vitiligo are more prone to psychological disorders. As of now, various...

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Autores principales: Srivastava, Priyansh, Choudhury, Alakto, Talwar, Mehak, Mohanty, Sabyasachi, Narad, Priyanka, Sengupta, Abhishek
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7246032/
https://www.ncbi.nlm.nih.gov/pubmed/32509450
http://dx.doi.org/10.7717/peerj.9119
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author Srivastava, Priyansh
Choudhury, Alakto
Talwar, Mehak
Mohanty, Sabyasachi
Narad, Priyanka
Sengupta, Abhishek
author_facet Srivastava, Priyansh
Choudhury, Alakto
Talwar, Mehak
Mohanty, Sabyasachi
Narad, Priyanka
Sengupta, Abhishek
author_sort Srivastava, Priyansh
collection PubMed
description Vitiligo is a chronic asymptomatic disorder affecting melanocytes from the basal layer of the epidermis which leads to a patchy loss of skin color. Even though it is one of the neglected disease conditions, people suffering from vitiligo are more prone to psychological disorders. As of now, various studies have been done in order to project auto-immune implications as the root cause. To understand the complexity of vitiligo, we propose the Vitiligo Information Resource (VIRdb) that integrates both the drug-target and systems approach to produce a comprehensive repository entirely devoted to vitiligo, along with curated information at both protein level and gene level along with potential therapeutics leads. These 25,041 natural compounds are curated from Natural Product Activity and Species Source Database. VIRdb is an attempt to accelerate the drug discovery process and laboratory trials for vitiligo through the computationally derived potential drugs. It is an exhaustive resource consisting of 129 differentially expressed genes, which are validated through gene ontology and pathway enrichment analysis. We also report 22 genes through enrichment analysis which are involved in the regulation of epithelial cell differentiation. At the protein level, 40 curated protein target molecules along with their natural hits that are derived through virtual screening. We also demonstrate the utility of the VIRdb by exploring the Protein–Protein Interaction Network and Gene–Gene Interaction Network of the target proteins and differentially expressed genes. For maintaining the quality and standard of the data in the VIRdb, the gold standard in bioinformatics toolkits like Cytoscape, Schrödinger’s GLIDE, along with the server installation of MATLAB, are used for generating results. VIRdb can be accessed through “http://www.vitiligoinfores.com/”.
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spelling pubmed-72460322020-06-04 VIRdb: a comprehensive database for interactive analysis of genes/proteins involved in the pathogenesis of vitiligo Srivastava, Priyansh Choudhury, Alakto Talwar, Mehak Mohanty, Sabyasachi Narad, Priyanka Sengupta, Abhishek PeerJ Bioinformatics Vitiligo is a chronic asymptomatic disorder affecting melanocytes from the basal layer of the epidermis which leads to a patchy loss of skin color. Even though it is one of the neglected disease conditions, people suffering from vitiligo are more prone to psychological disorders. As of now, various studies have been done in order to project auto-immune implications as the root cause. To understand the complexity of vitiligo, we propose the Vitiligo Information Resource (VIRdb) that integrates both the drug-target and systems approach to produce a comprehensive repository entirely devoted to vitiligo, along with curated information at both protein level and gene level along with potential therapeutics leads. These 25,041 natural compounds are curated from Natural Product Activity and Species Source Database. VIRdb is an attempt to accelerate the drug discovery process and laboratory trials for vitiligo through the computationally derived potential drugs. It is an exhaustive resource consisting of 129 differentially expressed genes, which are validated through gene ontology and pathway enrichment analysis. We also report 22 genes through enrichment analysis which are involved in the regulation of epithelial cell differentiation. At the protein level, 40 curated protein target molecules along with their natural hits that are derived through virtual screening. We also demonstrate the utility of the VIRdb by exploring the Protein–Protein Interaction Network and Gene–Gene Interaction Network of the target proteins and differentially expressed genes. For maintaining the quality and standard of the data in the VIRdb, the gold standard in bioinformatics toolkits like Cytoscape, Schrödinger’s GLIDE, along with the server installation of MATLAB, are used for generating results. VIRdb can be accessed through “http://www.vitiligoinfores.com/”. PeerJ Inc. 2020-05-21 /pmc/articles/PMC7246032/ /pubmed/32509450 http://dx.doi.org/10.7717/peerj.9119 Text en © 2020 Srivastava et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Srivastava, Priyansh
Choudhury, Alakto
Talwar, Mehak
Mohanty, Sabyasachi
Narad, Priyanka
Sengupta, Abhishek
VIRdb: a comprehensive database for interactive analysis of genes/proteins involved in the pathogenesis of vitiligo
title VIRdb: a comprehensive database for interactive analysis of genes/proteins involved in the pathogenesis of vitiligo
title_full VIRdb: a comprehensive database for interactive analysis of genes/proteins involved in the pathogenesis of vitiligo
title_fullStr VIRdb: a comprehensive database for interactive analysis of genes/proteins involved in the pathogenesis of vitiligo
title_full_unstemmed VIRdb: a comprehensive database for interactive analysis of genes/proteins involved in the pathogenesis of vitiligo
title_short VIRdb: a comprehensive database for interactive analysis of genes/proteins involved in the pathogenesis of vitiligo
title_sort virdb: a comprehensive database for interactive analysis of genes/proteins involved in the pathogenesis of vitiligo
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7246032/
https://www.ncbi.nlm.nih.gov/pubmed/32509450
http://dx.doi.org/10.7717/peerj.9119
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