RECTA: Regulon Identification Based on Comparative Genomics and Transcriptomics Analysis

Genes
Xin ChenQin Ma

Abstract

Regulons, which serve as co-regulated gene groups contributing to the transcriptional regulation of microbial genomes, have the potential to aid in understanding of underlying regulatory mechanisms. In this study, we designed a novel computational pipeline, regulon identification based on comparative genomics and transcriptomics analysis (RECTA), for regulon prediction related to the gene regulatory network under certain conditions. To demonstrate the effectiveness of this tool, we implemented RECTA on Lactococcus lactis MG1363 data to elucidate acid-response regulons. A total of 51 regulons were identified, 14 of which have computational-verified significance. Among these 14 regulons, five of them were computationally predicted to be connected with acid stress response. Validated by literature, 33 genes in Lactococcus lactis MG1363 were found to have orthologous genes which were associated with six regulons. An acid response related regulatory network was constructed, involving two trans-membrane proteins, eight regulons (llrA, llrC, hllA, ccpA, NHP6A, rcfB, regulons #8 and #39), nine functional modules, and 33 genes with orthologous genes known to be associated with acid stress. The predicted response pathways could serve as ...Continue Reading

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Datasets Mentioned

BETA
AM406671
GSE47012

Methods Mentioned

BETA
phylogenetic footprinting
footprinting
genetic modification

Software Mentioned

BLAST
TOMTOM
DOOR2
RECTA
MEME Suite
BBC
LOWESS
JASPAR
Motif Prediction by Phylogenetic footprinting ( MP3
DMINDA

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