VisANT-Predictome Interaction Statistics

In addition to the computational predicted interactions produced in our Lab, Predictome database also collects experimentally determined ones by either directly importing from literatures, or by synchronizing with existing interaction databases such as Biogrid, MINT,  BIND, MIPS etc. The integration of the interaction is gene-based, meaning that two protein nodes will be recognized as a single protein, if the same gene encodes them. This decision not to distinguish gene nodes from protein nodes was based primarily on the following observations:

• Independently created interaction databases often use different naming systems for proteins/genes. For example, MINT uses a proteins UniProt id in protein-protein interaction for Homo sapiens which, however, is represented using genes HGNC (HUGO Gene Nomenclature Committee) id in Biogrid.
• Genetic associations very often need to be compared to protein-protein interactions.
• High throughput gene expression results must often be mapped onto a protein-protein interaction network or pathway.

Because genes often encode multiple proteins, using gene id to represent both gene and protein is a natural choice; otherwise, uncertainty may arise when integrating interaction data. For example, for a gene with two splice variants, the variant to use when integrating interactions between the MINT (protein-based) and Biogrid databases (gene-based) will be ambiguous. The shortcoming of this solution is that certain splice variants may only share a subset of interactions. This dilemma can be overcome if alternative splicing knowledge is represented using a metanode, an undergoing process of this project.