Linked Life Data

16755590

Source:http://linkedlifedata.com/resource/pubmed/id/16755590

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
3
pubmed:dateCreated
2006-8-21
pubmed:abstractText
Operons are clusters of genes that are transcribed as a single message, and regulated by the same gene expression machinery. They are found primarily in prokaryotic genomes. Because genes in the same operon are likely to have related functions, identification of the operon structure is potentially useful for assigning gene function. We report the development and benchmarking of two different methods for detecting operons, based on an analysis of 42 fully sequenced prokaryotic organisms. The Gene Neighbor method (GNM) utilizes the relatively high conservation of gene order in operons, compared with genes in general. The Gene Gap Method (GGM) makes use of the relatively short gap between genes in operons compared with that otherwise found between adjacent genes. The methods have been benchmarked using KEGG pathway data and RegulonDB Escherichia coli operon data. With optimum parameters, the specificity of the GNM is 93% and the sensitivity is 70%. For the GGM, the specificity is 95% and the sensitivity is 68%. Together, the two methods have a sensitivity of 87.2%, while joint predictions have a sensitivity of 50% and a specificity of 98%. The methods are used to infer possible functions for some hypothetical genes in prokaryotic genomes. The methods have proven a useful addition to structure information in deriving protein function in a structural genomics project.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:status
MEDLINE
pubmed:month
Aug
pubmed:issn
1097-0134
pubmed:author
pubmed:issnType
Electronic
pubmed:day
15
pubmed:volume
64
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
615-28
pubmed:dateRevised
2007-11-14
pubmed:meshHeading
pubmed:year
2006
pubmed:articleTitle
Detection of operons.
pubmed:affiliation
Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA.
pubmed:publicationType
Journal Article, Research Support, N.I.H., Extramural