Systems biology research is like solving a puzzle: the goal is to figure out how the various parts interact and work together. The interactome of an organism is then analogous to the puzzle’s key: it describes the network of all the protein–protein interactions (PPIs). As such, identifying all the PPIs for an organism is of great value. Despite the use of high-throughput techniques in discovering PPIs, however, the coverage of experimentally determined PPI data remains poor. Such low coverage is partly because the set of possible PPIs to be verified is so large that any exhaustive experimental verification will take a long time, even with high-throughput techniques.
An open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization. Additional features are available as Apps (formerly called Plugins). Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases.
Aims to proteomics data analyses. Perseus extracts biologically meaningful information from processed raw files. It uses bioinformatic analyses from MaxQuant output and completes the proteomics analysis pipeline. It contains various statistical methods or illustrations (data transformation, normalization, imputation, and more). This tool gets five main interfaces: (1) data upload, (2) export, (3) processing, (4) analysis and (5) multimatrix handling.
Serves for the functional analysis of gene expression and genomic data. Babelomics offers the possibility to explore the effects of alteration in gene expression levels or changes in genes sequences within a functional context. It provides user-friendly access to a full range of methods that cover: (1) primary data analysis; (2) a variety of tests for different experimental designs; and (3) different enrichment and network analysis algorithms for the interpretation of the results of such tests in the proper functional context.
A framework dedicated to the structural analysis of protein interaction networks. SAPIN first identifies the protein parts that could be involved in the interaction and provides template structures. Next, SAPIN performs structural superimpositions to identify compatible and mutually exclusive interactions. Finally, the results are displayed using Cytoscape Web.
It was created by the Human Proteome Organization Proteomics Standards Initiative (HUPO-PSI) to enable computational access to molecular-interaction data resources by means of a standard Web Service and query language. Currently providing >150 million binary interaction evidences from 28 servers globally, the PSICQUIC interface allows the concurrent search of multiple molecular-interaction information resources using a single query.
Finds gene sets with statistically significant changes in functional protein-protein interactions. KEDDY is a statistical test for the differential functional protein-protein interactions (PPIs) of a set of genes between two conditions, with the use of known functional PPI information. The software can identify largely alternative gene sets with those from methods that evaluate expression changes. It was applied to two TCGA cancer gene expression data, glioblastoma multiforme (GBM) and breast cancer.
An online tool for identification of micorRNA-mediated module which is formed by protein-protein interactions (PPIs). Mirin integrates microRNA regulations and PPIs with microRNA/mRNA expression data to identify the perturbed microRNA regulatory modules and reveals their functional roles in specific biological conditions.