TranscriptomeBrowser 3.0 : introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks
| العنوان: | TranscriptomeBrowser 3.0 : introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks |
|---|---|
| المؤلفون: | Narayanan B. Perumal, Jean Imbert, Cyrille Lepoivre, Denis Puthier, Fabrice Lopez, Aurélie Bergon, Catherine Nguyen |
| المساهمون: | Technologies avancées pour le génôme et la clinique (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Transcriptomic Genomic Marseille-Luminy (TGML), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Translational Science, Eli Lilly and Company, Ecole Supérieure d'Ingénieurs de Luminy (ESIL), Université de la Méditerranée - Aix-Marseille 2, This work was supported by the Institut National de la Santé et de la Recherche Médicale (Inserm), the Canceropôle PACA and Marseille-Nice Genopole®. Authors acknowledge financial support from the EU ERASysBio Plus ModHeart project. Fabrice Lopez was supported by a fellowship from the EU STREP grant Diamonds and through funding from the IntegraTCell project (ANR, National Research Agency)., ANR-06-BYOS-0006,IntegraTcells,Analyse et Modélisation Intégrative du Développement des Lymphocytes T(2006), European Project: 32785,ERASYSBIO, BMC, Ed., Biologie systémique (BIOSYS) - Analyse et Modélisation Intégrative du Développement des Lymphocytes T - - IntegraTcells2006 - ANR-06-BYOS-0006 - BIOSYS - VALID, Systems Sciences - ERASYSBIO - 32785 - OLD, Technologies avancées pour le génôme et la clinique ( TAGC ), Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), ANR-06-BYOS-0006,IntegraTcells,Analyse et Modélisation Intégrative du Développement des Lymphocytes T ( 2006 ) |
| المصدر: | BMC Bioinformatics BMC Bioinformatics, 2012, 13 (1), pp.19. ⟨10.1186/1471-2105-13-19⟩ BMC Bioinformatics, BioMed Central, 2012, 13 (1), pp.19. ⟨10.1186/1471-2105-13-19⟩ BMC Bioinformatics, BioMed Central, 2012, 13 (1), pp.19. 〈10.1186/1471-2105-13-19〉 BMC Bioinformatics, Vol 13, Iss 1, p 19 (2012) |
| بيانات النشر: | HAL CCSD, 2012. |
| سنة النشر: | 2012 |
| مصطلحات موضوعية: | Gene regulatory network, Biological database, computer.software_genre, Biochemistry, [ SDV.CAN ] Life Sciences [q-bio]/Cancer, MESH : Proteins, Mice, User-Computer Interface, MESH : Thymocytes, Software, MESH : Dogs, Structural Biology, Databases, Genetic, Gene Regulatory Networks, [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], lcsh:QH301-705.5, Oligonucleotide Array Sequence Analysis, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], 0303 health sciences, Thymocytes, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH : Rats, Applied Mathematics, 030302 biochemistry & molecular biology, Cell Differentiation, Genomics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Computer Science Applications, MESH : Oligonucleotide Array Sequence Analysis, Knowledge base, lcsh:R858-859.7, Graph (abstract data type), [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Data mining, MESH : Software, MESH : Cell Differentiation, Biology, lcsh:Computer applications to medicine. Medical informatics, Set (abstract data type), 03 medical and health sciences, Dogs, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH : Mice, MESH : User-Computer Interface, Animals, Humans, Plug-in, MESH : Databases, Genetic, Molecular Biology, 030304 developmental biology, business.industry, Gene Expression Profiling, MESH : Gene Expression Profiling, MESH : Genomics, MESH : Humans, [ SDV.BC.BC ] Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Proteins, Rats, Visualization, lcsh:Biology (General), MESH : Gene Regulatory Networks, MESH : Animals, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, computer |
| الوصف: | Background Deciphering 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. Results We 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. Conclusions The 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. |
| وصف الملف: | application/pdf |
| اللغة: | English |
| تدمد: | 1471-2105 |
| DOI: | 10.1186/1471-2105-13-19⟩ |
| DOI: | 10.1186/1471-2105-13-19〉 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ae78b8ab544cb9ec22225628988148d0 https://www.hal.inserm.fr/inserm-00676438/file/1471-2105-13-19.pdf |
| Rights: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....ae78b8ab544cb9ec22225628988148d0 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 14712105 |
|---|---|
| DOI: | 10.1186/1471-2105-13-19⟩ |