Co-expressed gene assessment based on the path consistency algorithm: Operon detention in Escherichia coli

The assessment of co-expressed genes is an initial step to investigate the gene regulatory system in a microarray analysis. We designed a simple method to assess co-expressed genes from the expression profiles, based on the path consistency (PC) algorithm, which systematically infers a causal graph....

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Vydané v:2009 IEEE International Conference on Systems, Man and Cybernetics s. 4280 - 4286
Hlavní autori: Saito, S., Horimoto, K.
Médium: Konferenčný príspevok..
Jazyk:English
Vydavateľské údaje: IEEE 01.10.2009
Predmet:
Algorithm design and analysis
Biochemical analysis
Chemical technology
Clustering algorithms
co-expression
Computational biology
Computer industry
Cybernetics
Design methodology
gene expression profile
gene regulation
graphical model
Informatics
network inference
USA Councils
ISBN:9781424427932, 1424427932
ISSN:1062-922X
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Shrnutí:The assessment of co-expressed genes is an initial step to investigate the gene regulatory system in a microarray analysis. We designed a simple method to assess co-expressed genes from the expression profiles, based on the path consistency (PC) algorithm, which systematically infers a causal graph. The PC algorithm is simply modified for the frequent occurrence of high correlations between expression profiles, which causes an accidental stop of the algorithm by the violation of a numerical calculation. By utilizing the flexible features of the algorithm, biological information about co-expressed genes can be introduced into the algorithm. The performance is illustrated by the application to the gene profiles of operons: 1168 gene profiles in 137 known operons in Escherichia coli. By the improved algorithm, more than 80% of the operons were correctly detected, and less than one gene per operon was falsely detected. The performance promises the wide feasibility of the present method for the assessment of co-expressed genes from microarray data on a genomic scale.
ISBN:9781424427932
1424427932
ISSN:1062-922X
DOI:10.1109/ICSMC.2009.5346809