Wilson, GA;
Feil, EJ;
Lilley, AK;
Field, D;
(2007)
Large-scale comparative genomic ranking of taxonomically restricted genes (TRGs) in bacterial and archaeal genomes.
PLoS One
, 2
(3)
, Article e324. 10.1371/journal.pone.0000324.
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Abstract
BACKGROUND: Lineage-specific, or taxonomically restricted genes (TRGs), especially those that are species and strain-specific, are of special interest because they are expected to play a role in defining exclusive ecological adaptations to particular niches. Despite this, they are relatively poorly studied and little understood, in large part because many are still orphans or only have homologues in very closely related isolates. This lack of homology confounds attempts to establish the likelihood that a hypothetical gene is expressed and, if so, to determine the putative function of the protein. METHODOLOGY/PRINCIPAL FINDINGS: We have developed "QIPP" ("Quality Index for Predicted Proteins"), an index that scores the "quality" of a protein based on non-homology-based criteria. QIPP can be used to assign a value between zero and one to any protein based on comparing its features to other proteins in a given genome. We have used QIPP to rank the predicted proteins in the proteomes of Bacteria and Archaea. This ranking reveals that there is a large amount of variation in QIPP scores, and identifies many high-scoring orphans as potentially "authentic" (expressed) orphans. There are significant differences in the distributions of QIPP scores between orphan and non-orphan genes for many genomes and a trend for less well-conserved genes to have lower QIPP scores. CONCLUSIONS: The implication of this work is that QIPP scores can be used to further annotate predicted proteins with information that is independent of homology. Such information can be used to prioritize candidates for further analysis. Data generated for this study can be found in the OrphanMine at http://www.genomics.ceh.ac.uk/orphan_mine.
| Type: | Article |
|---|---|
| Title: | Large-scale comparative genomic ranking of taxonomically restricted genes (TRGs) in bacterial and archaeal genomes |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1371/journal.pone.0000324 |
| Publisher version: | http://dx.doi.org/10.1371/journal.pone.0000324 |
| Language: | English |
| Additional information: | © 2007 Wilson et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was funded through a Natural Environment Research Council Ph.D studentship awarded to GW (NER/S/A/2003/11341). |
| Keywords: | Archaea/classification Archaeal Proteins/genetics/standards Bacteria/classification Bacterial Proteins/genetics/standards Comparative Genomic Hybridization/*methods Escherichia coli K12/genetics Genome, Archaeal/*genetics Genome, Bacterial/*genetics Proteome/genetics |
| UCL classification: | UCL > Provost and Vice Provost Offices UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute > CRUK Cancer Trials Centre |
| URI: | https://discovery.ucl.ac.uk/id/eprint/1314930 |
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