Iis - Integrated Interactome System: A Web-based Platform For The Annotation, Analysis And Visualization Of Protein-metabolite-gene-drug Interactions By Integrating A Variety Of Data Sources And Tools

dc.creatorCarazzolle M.F.
dc.creatorDe Carvalho L.M.
dc.creatorSlepicka H.H.
dc.creatorVidal R.O.
dc.creatorPereira G.A.G.
dc.creatorKobarg J.
dc.creatorMeirelles G.V.
dc.date2014
dc.date2015-06-25T17:54:50Z
dc.date2015-11-26T14:36:25Z
dc.date2015-06-25T17:54:50Z
dc.date2015-11-26T14:36:25Z
dc.date.accessioned2018-03-28T21:40:13Z
dc.date.available2018-03-28T21:40:13Z
dc.identifier
dc.identifierPlos One. Public Library Of Science, v. 9, n. 6, p. - , 2014.
dc.identifier19326203
dc.identifier10.1371/journal.pone.0100385
dc.identifierhttp://www.scopus.com/inward/record.url?eid=2-s2.0-84903292701&partnerID=40&md5=ff61491bf9d66649f2b2b7e270ef6c57
dc.identifierhttp://www.repositorio.unicamp.br/handle/REPOSIP/86753
dc.identifierhttp://repositorio.unicamp.br/jspui/handle/REPOSIP/86753
dc.identifier2-s2.0-84903292701
dc.identifier.urihttp://repositorioslatinoamericanos.uchile.cl/handle/2250/1248739
dc.descriptionBackground: High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. Results: We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. Conclusions: We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/. © 2014 Carazzolle et al.
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dc.languageen
dc.publisherPublic Library of Science
dc.relationPLoS ONE
dc.rightsaberto
dc.sourceScopus
dc.titleIis - Integrated Interactome System: A Web-based Platform For The Annotation, Analysis And Visualization Of Protein-metabolite-gene-drug Interactions By Integrating A Variety Of Data Sources And Tools
dc.typeArtículos de revistas


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