title: 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 that the correlation between predicted and actual expression value is 0.467, which is similar to the microarray intra-array variation (p-value = 0.348), suggesting that intra-array variation accounts for a substantial portion of the transcriptome prediction error. In terms of predicting the effects of gene perturbation(s), our results suggest that the expression of 83% of the genes affected by perturbation can be predicted within 40% of error and the correlation between predicted and actual expression values among the affected genes to be 0.698. With the ability to predict the effects of gene perturbations, we demonstrated that our predictor has the potential to estimate the effects of varying gene expression level on the native transcriptome.
  
  
  CONCLUSIONS
  We present a potential means to predict an entire transcriptome and a tool to estimate the effects of gene perturbations for E. coli, which will aid biologists in hypothesis development. This study forms the baseline for future work in using gene co-expression network for gene expression prediction.
authors.affiliation: School of Chemical and Biomedical Engineering, Nanyang Technological University, Nanyang Ave, Singapore, Singapore. mauriceling@acm.org.
authors.forename: Maurice H T
authors.initials: MH
authors.lastname: Ling
authors.forename: Chueh Loo
authors.initials: CL
authors.lastname: Poh
mesh_terms: D010450:Endopeptidases / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D015964:Gene Expression Regulation, Bacterial; D055786:Gene Knockout Techniques; D053263:Gene Regulatory Networks; D020411:Oligonucleotide Array Sequence Analysis
chemical_list: D010450:Endopeptidases; C119558:hydrogenase maturating endopeptidase HYBD