SPECTRA: An Integrated Knowledge Base for Comparing Tissue and Tumor-Specific PPI Networks in Human.

Giovanni Micale,Rosalba Giugno,Alfredo Ferro,Alfredo Pulvirenti

doi:10.3389/fbioe.2015.00058

Abstract

Protein–protein interaction (PPI) networks available in public repositories usually represent relationships between proteins within the cell. They ignore the specific set of tissues or tumors where the interactions take place. Indeed, proteins can form tissue-selective complexes, while they remain inactive in other tissues. For these reasons, a great attention has been recently paid to tissue-specific PPI networks, in which nodes are proteins of the global PPI network whose corresponding genes are preferentially expressed in specific tissues. In this paper, we present SPECTRA, a knowledge base to build and compare tissue or tumor-specific PPI networks. SPECTRA integrates gene expression and protein interaction data from the most authoritative online repositories. We also provide tools for visualizing and comparing such networks, in order to identify the expression and interaction changes of proteins across tissues, or between the normal and pathological states of the same tissue. SPECTRA is available as a web server at http://alpha.dmi.unict.it/spectra.

Highlights

In the last 10 years, there has been a rapid growth of available protein–protein interaction (PPI) data
The architecture of SPECTRA is composed by (i) the searching tool, which allows to build Tissue-Specific PPI (TS-PPI); (ii) the comparison tool to look for shared differential expressions patterns between genes of two or more TS-PPI networks
SPECTRA Search Tool: Building TS-PPI Networks in SPECTRA SPECTRA builds TS-PPI networks starting from a user-defined set of genes, tissues, expression data, and interaction data

Summary

Introduction

In the last 10 years, there has been a rapid growth of available protein–protein interaction (PPI) data. They represent all known physical interactions between proteins within a cell. Primary sources of PPI data include BioGRID (Stark et al, 2006), DIP (Xenarios et al, 2000), HPRD (Peri et al, 2004), IntAct teorchard2013mintact, and MINT (Licata et al, 2012). DIP (Xenarios et al, 2000) was the first database, which combined information from multiple observations and experimental techniques into networks of interacting proteins for different species. MINT (Licata et al, 2012), which is based on the IntAct database

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Conclusion