Please use this identifier to cite or link to this item: https://hdl.handle.net/10356/103536
Title: A predictor for predicting Escherichia coli transcriptome and the effects of gene perturbations
Authors: Poh, Chueh Loo
Ling, Maurice H. T.
Keywords: DRNTU::Science::Medicine::Biomedical engineering
Issue Date: 2014
Source: Ling, M. H. T., & Poh, C. L. (2014). A predictor for predicting Escherichia coli transcriptome and the effects of gene perturbations. BMC Bioinformatics, 15(1), 140-.
Series/Report no.: BMC Bioinformatics
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. Conclusion 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.
URI: https://hdl.handle.net/10356/103536
http://hdl.handle.net/10220/20004
ISSN: 1471-2105
DOI: 10.1186/1471-2105-15-140
Rights: © 2014 Ling and Poh; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Fulltext Permission: open
Fulltext Availability: With Fulltext
Appears in Collections:SCBE Journal Articles

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