Differential enrichment of regulatory motifs in the composite network of protein-protein and gene regulatory interactions

BMC Systems Biology

Shekhar C Mande²  Khushbu Pal¹  Shubhada R Hegde² 

[1] Current Address: Cellworks Research India Ltd, Bangalore, India;Current Address: National Centre for Cell Science, NCCS Complex, University of Pune Campus, Ganeshkhind, Pune, Maharashtra 411007, India

关键词: Gene regulation;    Network;    Motifs;    Gene expression;    Protein-protein interaction;   

Others  :  1141335
DOI  :  10.1186/1752-0509-8-26

 received in 2013-08-03, accepted in 2014-02-17,  发布年份 2014

【 摘 要 】

Background

An important aspect of molecular interactions is the dynamics associated with growth conditions. Intuitively, not all possible interactions take place together all the time in a cell as only a subset of genes is expressed based on environmental conditions.

Results

Large scale gene expression data of Escherichia coli was analyzed to understand the dynamics exhibited at expression level. A large compendium of gene expression datasets, which covers about 466 growth conditions, was used for the analysis. Using gene expression data, genes of E. coli were profiled into three classes: Widely expressed, Conditionally expressed and Rarely expressed. Further, dynamics associated with molecular interactions were analysed by studying changing importance of motifs in the composite networks across growth conditions.

Conclusions

Our analysis of large scale gene expression data suggests conditional expression of genes which brings about befitting responses for a given growth environment. We observe a range of importance for network motifs across conditions which can be correlated with a specific function. Our study therefore suggests rewiring of molecular interactions driven by gene expression changes depending on the conditional needs.

【 授权许可】

   
2014 Hegde et al.; licensee BioMed Central Ltd.

【 图 表 】

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