Data mining in protein interactomics

In this article, protein interactomics, an emerging field that studies the total collection of proteins and intracellular protein interactions in an organism, i.e., the study of protein interactomes is introduced. Protein interactomics is concerned with all the expressed proteins in a given tissue or cell type and how proteins physically interact with, or bind to, one another in the protein interaction network. Protein interactomes can provide information about protein functional links and protein functional context not apparent from either protein sequence analysis or protein expression analysis. By studying protein interactomics, biologists can compile biological pathway models to understand functional roles of previously uncharacterized proteins and biological processes in different developmental and environmental conditions. The paper discussed new biological discovery opportunities by presenting six specific data mining challenges in protein interactomics - data generation, data representation, data cleansing, data integration, data analysis/visualization, and knowledge curation.