ProFuMCell and ProModb: web services for analyzing interaction-based functionally localized protein modules in a cell

Abstract

The modular organization of a cell which can be determined by its interaction network allows us to understand a mesh of cooperation among the functional modules. Therefore, cellular level identification of functional modules aids in understanding the functional and structural characteristics of the biological network of a cell and also assists in determining or comprehending the evolutionary signal. We develop ProFuM-Cell that performs real-time web scraping for generating clusters of the cellular level functional units of an organism. ProFuMCell constructs the Protein Locality Graphs and clusters the cellular level functional units of an organism by utilizing experimentally verified data from various online sources. Also, we develop ProModb, a database service that houses precomputed whole-cell protein-protein interaction network-based functional modules of an organism using ProFuMCell. Our web service is entirely synchronized with the KEGG pathway database and allows users to generate spatially localized protein modules for any organism belonging to the KEGG genome using its real-time web scraping characteristics. Hence, the server will host as many organisms as is maintained by the KEGG database. Our web services provide the users a comprehensive and integrated tool for an efficient browsing and extraction of the spatial locality-based protein locality graph and the functional modules constructed by gathering experimental data from several interaction databases and pathway maps. We believe that our web services will be beneficial in pharmacological research, where a novel research domain called modular pharmacology has initiated the study on the diagnosis, prevention, and treatment of deadly diseases using functional modules. Graphical TOC Entry O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/446966v2_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@145374borg.highwire.dtl.DTLVardef@13121aeorg.highwire.dtl.DTLVardef@9a3681org.highwire.dtl.DTLVardef@707985_HPS_FORMAT_FIGEXP M_FIG C_FIG