Computational protocol: Genetic Interaction Maps in Escherichia coli Reveal Functional Crosstalk among Cell Envelope Biogenesis Pathways

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Protocol publication

[…] Plate image processing and colony size quantization were adapted from an automated image processing system originally devised for yeast . Epistasis scores were calculated based on a multiplicative model where a GI between a pair of genes (i, j) is identified if the fitness phenotype of the double mutant (Wij) deviates significantly from that predicted for non-interacting gene pairs (Wi×Wj). Enrichment was determined by contrasting the frequency of observed genetic interactions between or within functional modules against the expected frequencies according to the hypergeometric distribution using the Fisher's exact test with correction for multiple hypothesis testing . This enrichment approach was used to determine the optimal E-score cutoff values for selecting aggravating and alleviating genetic interactions. Additional details are provided in Protocols , , , , , .Computational prediction of regulatory sRNA targets was performed using RNAup from the Vienna RNA package (-Xp-w20-b parameters) to measure sequence complementarity between each sncRNA and the 5′ regions (−50 and +50 nt relative to translation start site) of all protein coding genes in E. coli. Genes were ranked according to free energy, with the lowest scoring predicted as targets. Known mRNA targets were compiled from published functional studies and the NPInter and sRNAMap databases. […]

Pipeline specifications

Software tools RNAup, ViennaRNA
Databases NPInter sRNAMap
Application RNA structure analysis
Organisms Escherichia coli