Integrated Approach to Reconstruction of Microbial Regulatory Networks

Technical Report · Mon Nov 04 04:00:00 EST 2013

DOI:https://doi.org/10.2172/1098153· OSTI ID:1098153

Rodionov, Dmitry A ^[1]; Novichkov, Pavel S ^[2]

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1. Sanford-Burnham Medical Research Institute; Sanford-Burnham Medical Research Institute
2. Lawrence Berkeley National Laboratory

This project had the goal(s) of development of integrated bioinformatics platform for genome-scale inference and visualization of transcriptional regulatory networks (TRNs) in bacterial genomes. The work was done in Sanford-Burnham Medical Research Institute (SBMRI, P.I. D.A. Rodionov) and Lawrence Berkeley National Laboratory (LBNL, co-P.I. P.S. Novichkov). The developed computational resources include: (1) RegPredict web-platform for TRN inference and regulon reconstruction in microbial genomes, and (2) RegPrecise database for collection, visualization and comparative analysis of transcriptional regulons reconstructed by comparative genomics. These analytical resources were selected as key components in the DOE Systems Biology KnowledgeBase (SBKB). The high-quality data accumulated in RegPrecise will provide essential datasets of reference regulons in diverse microbes to enable automatic reconstruction of draft TRNs in newly sequenced genomes. We outline our progress toward the three aims of this grant proposal, which were: Develop integrated platform for genome-scale regulon reconstruction; Infer regulatory annotations in several groups of bacteria and building of reference collections of microbial regulons; and Develop KnowledgeBase on microbial transcriptional regulation.

• Research Organization: Sanford-Burnham Medical Research Institute, La Jolla, CA
• Sponsoring Organization: USDOE; USDOE SC Office of Biological and Environmental Research (SC-23)
• Contributing Organization: Lawrence Berkeley National Laboratory
• DOE Contract Number: SC0004999
• OSTI ID: 1098153
• Report Number(s): DOE-SBMRI-SC4999; Award Register#: ER65026
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
bacteria
genomics
transcriptional networks