The PPI data were downloaded from the Biological General Repository for Interaction Datasets (BioGRID), the Molecular INTeraction database (MINT), the IntAct molecular interaction database (IntAct), and the iRefIndex database.
For each pathway, a hyperlink enables the user to generate an interactive graph-based visualization of the sub-network representing the analysed datasets in the molecular interaction network.
There are several publicly available databases that contain predictive and experimental PPI information, including Biological General Repository for Interaction Datasets (BioGRID), Database of Interacting Proteins (DIP), Molecular Interactions Database (MINT), and Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) [ 1, 12].
Effective analysis and visualization tools for large-scale cellular networks that can draw connectivity diagrams with an unbiased predisposition from large interaction datasets can help cell and molecular biologists identify potential new pathways and sometimes predict missing components and interactions.
The PPI databases included in this analysis were: the Human Protein Reference Database (HPRD) [ 20], the general repository for interaction datasets (BioGRID) [ 21], and the Molecular INTeraction database (MINT) [ 22].
In recent years, high-throughput techniques in a genomic scale such as yeast-two-hybrid, mass spectrometry, and protein chip technologies have multiplied the volume of protein interaction datasets exponentially and also have provided us a genomic level view of molecular interactions.
Molecular interaction analysis and visualization of human orthologs of Kmar genes were done by using networks available from The Biological General Repository for Interaction Datasets (BioGRID) (thebiogrid.org) or the Unified Human Interactome (UniHI) (www.unihi.org) [ 27, 39].
In this work, we present MImerge and MIscore, which provide simple scoring heuristics for molecular interactions dependent on available interaction evidence, thus providing a framework to integrate and score literature curated interaction datasets.
Several databases have now been established as repositories for molecular interaction data including the Molecular Interaction database (MINT) [ 23]; the IntAct database [ 24]; the Database of Interacting Proteins (DIP) [ 25]; the General Repository for Interaction Datasets (BioGRID) [ 26] and the Biomolecular Interaction Network Database (BIND) [ 27].
The network was produced introducing the coexpression dataset of 615 genes and 2190 pairwise interactions in Cytoscape (a bioinformatics software platform for visualizing molecular interaction networks, [18].
