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HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency
Measuring the altered gene expression level and identifying differentially expressed genes/proteins during HIV infection, replication and latency is fundamental for broadening our understanding of the mechanisms of HIV infection and T-cell dysfunction. Such studies are crucial for developing effecti...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5371986/ https://www.ncbi.nlm.nih.gov/pubmed/28358052 http://dx.doi.org/10.1038/srep45509 |
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author | Li, Chen Ramarathinam, Sri H. Revote, Jerico Khoury, Georges Song, Jiangning Purcell, Anthony W. |
author_facet | Li, Chen Ramarathinam, Sri H. Revote, Jerico Khoury, Georges Song, Jiangning Purcell, Anthony W. |
author_sort | Li, Chen |
collection | PubMed |
description | Measuring the altered gene expression level and identifying differentially expressed genes/proteins during HIV infection, replication and latency is fundamental for broadening our understanding of the mechanisms of HIV infection and T-cell dysfunction. Such studies are crucial for developing effective strategies for virus eradication from the body. Inspired by the availability and enrichment of gene expression data during HIV infection, replication and latency, in this study, we proposed a novel compendium termed HIVed (HIV expression database; http://hivlatency.erc.monash.edu/) that harbours comprehensive functional annotations of proteins, whose genes have been shown to be dysregulated during HIV infection, replication and latency using different experimental designs and measurements. We manually curated a variety of third-party databases for structural and functional annotations of the protein entries in HIVed. With the goal of benefiting HIV related research, we collected a number of biological annotations for all the entries in HIVed besides their expression profile, including basic protein information, Gene Ontology terms, secondary structure, HIV-1 interaction and pathway information. We hope this comprehensive protein-centric knowledgebase can bridge the gap between the understanding of differentially expressed genes and the functions of their protein products, facilitating the generation of novel hypotheses and treatment strategies to fight against the HIV pandemic. |
format | Online Article Text |
id | pubmed-5371986 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-53719862017-03-31 HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency Li, Chen Ramarathinam, Sri H. Revote, Jerico Khoury, Georges Song, Jiangning Purcell, Anthony W. Sci Rep Article Measuring the altered gene expression level and identifying differentially expressed genes/proteins during HIV infection, replication and latency is fundamental for broadening our understanding of the mechanisms of HIV infection and T-cell dysfunction. Such studies are crucial for developing effective strategies for virus eradication from the body. Inspired by the availability and enrichment of gene expression data during HIV infection, replication and latency, in this study, we proposed a novel compendium termed HIVed (HIV expression database; http://hivlatency.erc.monash.edu/) that harbours comprehensive functional annotations of proteins, whose genes have been shown to be dysregulated during HIV infection, replication and latency using different experimental designs and measurements. We manually curated a variety of third-party databases for structural and functional annotations of the protein entries in HIVed. With the goal of benefiting HIV related research, we collected a number of biological annotations for all the entries in HIVed besides their expression profile, including basic protein information, Gene Ontology terms, secondary structure, HIV-1 interaction and pathway information. We hope this comprehensive protein-centric knowledgebase can bridge the gap between the understanding of differentially expressed genes and the functions of their protein products, facilitating the generation of novel hypotheses and treatment strategies to fight against the HIV pandemic. Nature Publishing Group 2017-03-30 /pmc/articles/PMC5371986/ /pubmed/28358052 http://dx.doi.org/10.1038/srep45509 Text en Copyright © 2017, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Li, Chen Ramarathinam, Sri H. Revote, Jerico Khoury, Georges Song, Jiangning Purcell, Anthony W. HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency |
title | HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency |
title_full | HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency |
title_fullStr | HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency |
title_full_unstemmed | HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency |
title_short | HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency |
title_sort | hived, a knowledgebase for differentially expressed human genes and proteins during hiv infection, replication and latency |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5371986/ https://www.ncbi.nlm.nih.gov/pubmed/28358052 http://dx.doi.org/10.1038/srep45509 |
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