TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks

BMC Bioinformatics

Software

Denis Puthier¹  Cyrille Lepoivre²  Aurélie Bergon²  Fabrice Lopez³  Jean Imbert³  Catherine Nguyen³  Narayanan B Perumal⁴ 

[1] TAGC UMR_S 928, Inserm, Parc Scientifique de Luminy, Marseille, France;ESIL, Universités de Provence et de la Méditerranée, Parc Scientifique de Luminy, Marseille, France;TAGC UMR_S 928, Inserm, Parc Scientifique de Luminy, Marseille, France;Université de la Méditerranée, AMU, Parc Scientifique de Luminy, Marseille, France;TAGC UMR_S 928, Inserm, Parc Scientifique de Luminy, Marseille, France;Université de la Méditerranée, AMU, Parc Scientifique de Luminy, Marseille, France;TGML, IBiSA Platform, Parc Scientifique de Luminy, Marseille, France;Translational Science, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, USA;

关键词: Gene Regulatory Network;    Phylogenetic Footprinting;    Position Weight Matrice;    Video Tutorial;    TFBS Prediction;   

DOI  :  10.1186/1471-2105-13-19

 received in 2011-12-07, accepted in 2012-01-31,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundDeciphering gene regulatory networks by in silico approaches is a crucial step in the study of the molecular perturbations that occur in diseases. The development of regulatory maps is a tedious process requiring the comprehensive integration of various evidences scattered over biological databases. Thus, the research community would greatly benefit from having a unified database storing known and predicted molecular interactions. Furthermore, given the intrinsic complexity of the data, the development of new tools offering integrated and meaningful visualizations of molecular interactions is necessary to help users drawing new hypotheses without being overwhelmed by the density of the subsequent graph.ResultsWe extend the previously developed TranscriptomeBrowser database with a set of tables containing 1,594,978 human and mouse molecular interactions. The database includes: (i) predicted regulatory interactions (computed by scanning vertebrate alignments with a set of 1,213 position weight matrices), (ii) potential regulatory interactions inferred from systematic analysis of ChIP-seq experiments, (iii) regulatory interactions curated from the literature, (iv) predicted post-transcriptional regulation by micro-RNA, (v) protein kinase-substrate interactions and (vi) physical protein-protein interactions. In order to easily retrieve and efficiently analyze these interactions, we developed In-teractomeBrowser, a graph-based knowledge browser that comes as a plug-in for Transcriptome-Browser. The first objective of InteractomeBrowser is to provide a user-friendly tool to get new insight into any gene list by providing a context-specific display of putative regulatory and physical interactions. To achieve this, InteractomeBrowser relies on a "cell compartments-based layout" that makes use of a subset of the Gene Ontology to map gene products onto relevant cell compartments. This layout is particularly powerful for visual integration of heterogeneous biological information and is a productive avenue in generating new hypotheses. The second objective of InteractomeBrowser is to fill the gap between interaction databases and dynamic modeling. It is thus compatible with the network analysis software Cytoscape and with the Gene Interaction Network simulation software (GINsim). We provide examples underlying the benefits of this visualization tool for large gene set analysis related to thymocyte differentiation.ConclusionsThe InteractomeBrowser plugin is a powerful tool to get quick access to a knowledge database that includes both predicted and validated molecular interactions. InteractomeBrowser is available through the TranscriptomeBrowser framework and can be found at: http://tagc.univ-mrs.fr/tbrowser/. Our database is updated on a regular basis.

【 授权许可】

Unknown   
© Lepoivre et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.