NetGenes: A Database of Essential Genes Predicted Using Features From Interaction Networks

Essential gene prediction models built so far are heavily reliant on sequence-based features, and the scope of network-based features has been narrow. Previous work from our group demonstrated the importance of using network-based features for predicting essential genes with high accuracy. Here, we...

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Autores principales: Senthamizhan, Vimaladhasan, Ravindran, Balaraman, Raman, Karthik
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Genetics
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8495214/
https://www.ncbi.nlm.nih.gov/pubmed/34630517
http://dx.doi.org/10.3389/fgene.2021.722198
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author Senthamizhan, Vimaladhasan
Ravindran, Balaraman
Raman, Karthik
author_facet Senthamizhan, Vimaladhasan
Ravindran, Balaraman
Raman, Karthik
author_sort Senthamizhan, Vimaladhasan
collection PubMed
description Essential gene prediction models built so far are heavily reliant on sequence-based features, and the scope of network-based features has been narrow. Previous work from our group demonstrated the importance of using network-based features for predicting essential genes with high accuracy. Here, we apply our approach for the prediction of essential genes to organisms from the STRING database and host the results in a standalone website. Our database, NetGenes, contains essential gene predictions for 2,700+ bacteria predicted using features derived from STRING protein–protein functional association networks. Housing a total of over 2.1 million genes, NetGenes offers various features like essentiality scores, annotations, and feature vectors for each gene. NetGenes database is available from https://rbc-dsai-iitm.github.io/NetGenes/.
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spelling pubmed-84952142021-10-08 NetGenes: A Database of Essential Genes Predicted Using Features From Interaction Networks Senthamizhan, Vimaladhasan Ravindran, Balaraman Raman, Karthik Front Genet Genetics Essential gene prediction models built so far are heavily reliant on sequence-based features, and the scope of network-based features has been narrow. Previous work from our group demonstrated the importance of using network-based features for predicting essential genes with high accuracy. Here, we apply our approach for the prediction of essential genes to organisms from the STRING database and host the results in a standalone website. Our database, NetGenes, contains essential gene predictions for 2,700+ bacteria predicted using features derived from STRING protein–protein functional association networks. Housing a total of over 2.1 million genes, NetGenes offers various features like essentiality scores, annotations, and feature vectors for each gene. NetGenes database is available from https://rbc-dsai-iitm.github.io/NetGenes/. Frontiers Media S.A. 2021-09-23 /pmc/articles/PMC8495214/ /pubmed/34630517 http://dx.doi.org/10.3389/fgene.2021.722198 Text en Copyright © 2021 Senthamizhan, Ravindran and Raman. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Senthamizhan, Vimaladhasan
Ravindran, Balaraman
Raman, Karthik
NetGenes: A Database of Essential Genes Predicted Using Features From Interaction Networks
title NetGenes: A Database of Essential Genes Predicted Using Features From Interaction Networks
title_full NetGenes: A Database of Essential Genes Predicted Using Features From Interaction Networks
title_fullStr NetGenes: A Database of Essential Genes Predicted Using Features From Interaction Networks
title_full_unstemmed NetGenes: A Database of Essential Genes Predicted Using Features From Interaction Networks
title_short NetGenes: A Database of Essential Genes Predicted Using Features From Interaction Networks
title_sort netgenes: a database of essential genes predicted using features from interaction networks
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8495214/
https://www.ncbi.nlm.nih.gov/pubmed/34630517
http://dx.doi.org/10.3389/fgene.2021.722198
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AT ramankarthik netgenesadatabaseofessentialgenespredictedusingfeaturesfrominteractionnetworks

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