IIS

The Integrated Interactome System (IIS) is a software tool designed to simplify the analysis of physical, genetic, and chemical-genetic interactions in Systems Biology. This tool is an integrative platform with a user-friendly web-based interface that allows for the annotation, analysis, and visualization of the interaction profiles of proteins/genes, metabolites, and drugs of interest.

IIS works through four connected modules that enable the user to comprehensively analyze their data. The Submission module receives the raw data derived from Sanger sequencing, which is then processed and analyzed through the Search module. This module allows the user to search for processed reads to be assembled into contigs/singlets or for lists of proteins/genes, metabolites, and drugs of interest, which are added to the project.

The Annotation module assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with an automatic annotation that can be manually curated by the user. Finally, the Interactome module maps the contigs/singlets or the uploaded lists to entries in the 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 an XGMML file that can be imported into Cytoscape or be visualized directly on the web.

The development of IIS was based on integrating diverse databases that were needed to create appropriate tools for a systematic analysis of physical, genetic, and chemical-genetic interactions. The tool has been validated with yeast two-hybrid, proteomics, and metabolomics datasets but is also extendable to other datasets.

Topic

Protein interactions;Drug discovery;Data visualisation;Molecular interactions, pathways and networks

Detail

  • Operation: Pathway or network analysis;Gene functional annotation;Pathway or network visualisation

  • Software interface: Web user interface

  • Language: Perl, PHP

  • License: -

  • Cost: Free

  • Version name: 1.0.0.0

  • Credit: Fundação de Amparo à Pesquisa do Estado São Paulo (FAPESP), Conselho Nacional de Pesquisa e Desenvolvimento (CNPq), Brazilian Biosciences National Laboratory (LNBio) and Center for Computational Engineering and Sciences at UNICAMP-Brazil.

  • Input: -

  • Output: -

  • Contact: support_iis@lge.ibi.unicamp.br

  • Collection: -

  • Maturity: -

Publications

  • 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.
  • Carazzolle MF, et al. 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. 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. 2014; 9:e100385. doi: 10.1371/journal.pone.0100385
  • https://doi.org/10.1371/journal.pone.0100385
  • PMID: 24949626
  • PMC: PMC4065059

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