title: Differential enrichment of regulatory motifs in the composite network of protein-protein and gene regulatory interactions.
abstract: 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.
authors.forename: Shubhada R
authors.initials: SR
authors.lastname: Hegde
authors.forename: Khushbu
authors.initials: K
authors.lastname: Pal
authors.affiliation: Centre for DNA Fingerprinting and Diagnostics, Bldg 7, Gruhakalpa, 5-4-399/B, Nampally, Hyderabad 500 001, India. shekhar@nccs.res.in.
authors.forename: Shekhar C
authors.initials: SC
authors.lastname: Mande
mesh_terms: D019295:Computational Biology; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D060066:Protein Interaction Maps
chemical_list: D029968:Escherichia coli Proteins