Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in <it>Streptomyces coelicolor</it>
<p>Abstract</p> <p>Background</p> <p><it>Streptomyces coelicolor</it>, a model organism of antibiotic producing bacteria, has one of the largest genomes of the bacterial kingdom, including 7825 predicted protein coding genes. A large number of these genes, n...
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doaj-08568912a0ed4baa86f15e8c96b9c92f2020-11-25T02:47:49ZengBMCBMC Research Notes1756-05002011-09-014132510.1186/1756-0500-4-325Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in <it>Streptomyces coelicolor</it>Takano ErikoAlam MohammadBreitling Rainer<p>Abstract</p> <p>Background</p> <p><it>Streptomyces coelicolor</it>, a model organism of antibiotic producing bacteria, has one of the largest genomes of the bacterial kingdom, including 7825 predicted protein coding genes. A large number of these genes, nearly 34%, are functionally orphan (hypothetical proteins with unknown function). However, in gene expression time course data, many of these functionally orphan genes show interesting expression patterns.</p> <p>Results</p> <p>In this paper, we analyzed all functionally orphan genes of <it>Streptomyces coelicolor </it>and identified a list of "high priority" orphans by combining gene expression analysis and additional phylogenetic information (i.e. the level of evolutionary conservation of each protein).</p> <p>Conclusions</p> <p>The prioritized orphan genes are promising candidates to be examined experimentally in the lab for further characterization of their function.</p> http://www.biomedcentral.com/1756-0500/4/325 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Takano Eriko Alam Mohammad Breitling Rainer |
spellingShingle |
Takano Eriko Alam Mohammad Breitling Rainer Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in <it>Streptomyces coelicolor</it> BMC Research Notes |
author_facet |
Takano Eriko Alam Mohammad Breitling Rainer |
author_sort |
Takano Eriko |
title |
Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in <it>Streptomyces coelicolor</it> |
title_short |
Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in <it>Streptomyces coelicolor</it> |
title_full |
Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in <it>Streptomyces coelicolor</it> |
title_fullStr |
Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in <it>Streptomyces coelicolor</it> |
title_full_unstemmed |
Prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in <it>Streptomyces coelicolor</it> |
title_sort |
prioritizing orphan proteins for further study using phylogenomics and gene expression profiles in <it>streptomyces coelicolor</it> |
publisher |
BMC |
series |
BMC Research Notes |
issn |
1756-0500 |
publishDate |
2011-09-01 |
description |
<p>Abstract</p> <p>Background</p> <p><it>Streptomyces coelicolor</it>, a model organism of antibiotic producing bacteria, has one of the largest genomes of the bacterial kingdom, including 7825 predicted protein coding genes. A large number of these genes, nearly 34%, are functionally orphan (hypothetical proteins with unknown function). However, in gene expression time course data, many of these functionally orphan genes show interesting expression patterns.</p> <p>Results</p> <p>In this paper, we analyzed all functionally orphan genes of <it>Streptomyces coelicolor </it>and identified a list of "high priority" orphans by combining gene expression analysis and additional phylogenetic information (i.e. the level of evolutionary conservation of each protein).</p> <p>Conclusions</p> <p>The prioritized orphan genes are promising candidates to be examined experimentally in the lab for further characterization of their function.</p> |
url |
http://www.biomedcentral.com/1756-0500/4/325 |
work_keys_str_mv |
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