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EvoCor: a platform for predicting functionally related genes using phylogenetic and expression profiles

The wealth of publicly available gene expression and genomic data provides unique opportunities for computational inference to discover groups of genes that function to control specific cellular processes. Such genes are likely to have co-evolved and be expressed in the same tissues and cells. Unfor...

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Autores principales: Dittmar, W. James, McIver, Lauren, Michalak, Pawel, Garner, Harold R., Valdez, Gregorio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086105/
https://www.ncbi.nlm.nih.gov/pubmed/24848012
http://dx.doi.org/10.1093/nar/gku442
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author Dittmar, W. James
McIver, Lauren
Michalak, Pawel
Garner, Harold R.
Valdez, Gregorio
author_facet Dittmar, W. James
McIver, Lauren
Michalak, Pawel
Garner, Harold R.
Valdez, Gregorio
author_sort Dittmar, W. James
collection PubMed
description The wealth of publicly available gene expression and genomic data provides unique opportunities for computational inference to discover groups of genes that function to control specific cellular processes. Such genes are likely to have co-evolved and be expressed in the same tissues and cells. Unfortunately, the expertise and computational resources required to compare tens of genomes and gene expression data sets make this type of analysis difficult for the average end-user. Here, we describe the implementation of a web server that predicts genes involved in affecting specific cellular processes together with a gene of interest. We termed the server ‘EvoCor’, to denote that it detects functional relationships among genes through evolutionary analysis and gene expression correlation. This web server integrates profiles of sequence divergence derived by a Hidden Markov Model (HMM) and tissue-wide gene expression patterns to determine putative functional linkages between pairs of genes. This server is easy to use and freely available at http://pilot-hmm.vbi.vt.edu/.
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spelling pubmed-40861052014-10-28 EvoCor: a platform for predicting functionally related genes using phylogenetic and expression profiles Dittmar, W. James McIver, Lauren Michalak, Pawel Garner, Harold R. Valdez, Gregorio Nucleic Acids Res Article The wealth of publicly available gene expression and genomic data provides unique opportunities for computational inference to discover groups of genes that function to control specific cellular processes. Such genes are likely to have co-evolved and be expressed in the same tissues and cells. Unfortunately, the expertise and computational resources required to compare tens of genomes and gene expression data sets make this type of analysis difficult for the average end-user. Here, we describe the implementation of a web server that predicts genes involved in affecting specific cellular processes together with a gene of interest. We termed the server ‘EvoCor’, to denote that it detects functional relationships among genes through evolutionary analysis and gene expression correlation. This web server integrates profiles of sequence divergence derived by a Hidden Markov Model (HMM) and tissue-wide gene expression patterns to determine putative functional linkages between pairs of genes. This server is easy to use and freely available at http://pilot-hmm.vbi.vt.edu/. Oxford University Press 2014-07-01 2014-05-21 /pmc/articles/PMC4086105/ /pubmed/24848012 http://dx.doi.org/10.1093/nar/gku442 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Article
Dittmar, W. James
McIver, Lauren
Michalak, Pawel
Garner, Harold R.
Valdez, Gregorio
EvoCor: a platform for predicting functionally related genes using phylogenetic and expression profiles
title EvoCor: a platform for predicting functionally related genes using phylogenetic and expression profiles
title_full EvoCor: a platform for predicting functionally related genes using phylogenetic and expression profiles
title_fullStr EvoCor: a platform for predicting functionally related genes using phylogenetic and expression profiles
title_full_unstemmed EvoCor: a platform for predicting functionally related genes using phylogenetic and expression profiles
title_short EvoCor: a platform for predicting functionally related genes using phylogenetic and expression profiles
title_sort evocor: a platform for predicting functionally related genes using phylogenetic and expression profiles
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086105/
https://www.ncbi.nlm.nih.gov/pubmed/24848012
http://dx.doi.org/10.1093/nar/gku442
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