A predictor for predicting Escherichia coli transcriptome and the effects of gene perturbations.

ABSTRACT:

Background

A means to predict the effects of gene over-expression, knockouts, and environmental stimuli in silico is useful for system biologists to develop and test hypotheses. Several studies had predicted the expression of all Escherichia coli genes from sequences and reported a correlation of 0.301 between predicted and actual expression. However, these do not allow biologists to study the effects of gene perturbations on the native transcriptome.

Results

We developed a predictor to predict transcriptome-scale gene expression from a small number (n = 59) of known gene expressions using gene co-expression network, which can be used to predict the effects of over-expressions and knockdowns on E. coli transcriptome. In terms of transcriptome prediction, our results show tha

SUBMITTER: Ling MH 

PROVIDER: S-EPMC4038595 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature