ENVIRONMENTAL DEPENDENCY OF GENE KNOCKOUTS ON PHENOTYPE MICROARRAY ANALYSIS IN ESCHERICHIA COLI
Systematic studies have revealed that single gene deletions often display little phenotypic e.ects under laboratory conditions and that in many cases gene dispensability depends on the experimental conditions. To elucidate the environmental dependency of genes, we analyzed the e.ects of gene deletions by Phenotype MicroArrayTM (PM), a system for quantitative screening of thousands of phenotypes in a high-throughput manner. Here, we proposed a new statistical approach to minimize error inherent in measurements of low respiration rates and. nd which mutants showed signi.cant phenotypic changes in comparison to the wild-type. We show analyzing results from comprehensive PM assays of 298 single-gene knockout mutants in the Keio collection and two additional mutants under 1,920 di.erent conditions. We focused on isozymes of these genes as simple duplications and analyzed correlations between phenotype changes and proteinexpression levels. Our results revealed divergence of the environmental dependency of the gene among the knockout genes and have also given some insights into possibilities of alternative pathways and availabilities of information on protein synthesis patterns to classify or predict functions of target genes from systematic phenotype screening.
Phenotype MicroArray phenotype protein synthesis robustness Escherichia coli
YUKAKO TOHSATO TOMOYA BABA YUSAKU MAZAKI MASAHIRO ITO BARRY L. WANNER HIROTADA MORI
Department of Bioinformatics, Ritsumeikan University 1-1-1 Nojihigashi, Kusatu, Shiga 525-8577,Japan Transdisciplinary Research Integration Center Research Organization of Information and Systems 1111 Department of Biological Sciences, Purdue University West Lafayette, IN 47907-2054, USA Graduate School of Biological Sciences Nara Institute of Science and Technology 8916-5 Takayama, Iko
国际会议
上海
英文
329-345
2010-12-06（万方平台首次上网日期，不代表论文的发表时间）