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

Author(s)

Carazzolle, Marcelo Falsarella ^{[1, 2]} ; de Carvalho, Lucas Miguel ^[1] ; Slepicka, Hugo Henrique ^[3] ; Vidal, Ramon Oliveira ^[2] ; Guimaraes Pereira, Goncalo Amarante ^[2] ; Kobarg, Joerg ^[1] ; Meirelles, Gabriela Vaz ^[1]

Affiliation

^[1] Ctr Nacl Pesquisa Energia & Mat, Lab Nacl Biociencias, Sao Paulo - Brazil

^[2] Univ Estadual Campinas, Inst Biol, Dept Genet & Evolucao, Lab Genom & Expressao, Sao Paulo - Brazil

^[3] Ctr Nacl Pesquisa Energia & Mat, Lab Nacl Luz Sincrotron, Sao Paulo - Brazil

• Document type: Journal article
• Source: PLoS One; v. 9, n. 6 JUN 20 2014.
• Web of Science Citations: 27

Abstract

Background: 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/. (AU)

• FAPESP's process: 13/08293-7 - CCES - Center for Computational Engineering and Sciences
• Grantee: Munir Salomao Skaf
• Support type: Research Grants - Research, Innovation and Dissemination Centers - RIDC