R. Chowdhary, S.L. Tan, J. Zhang, S. Karnik, V.B. Bajic, J.S. Liu
PLoS One, 7(4):e34480, (2012)
Background
Protein
interaction networks (PINs) specific within a particular context
contain crucial information regarding many cellular biological
processes. For example, PINs may include information on the type and
directionality of interaction (e.g. phosphorylation), location of
interaction (i.e. tissues, cells), and related diseases. Currently, very
few tools are capable of deriving context-specific PINs for conducting
exploratory analysis.
Results
We
developed a literature-based online system, Context-specific Protein
Network Miner (CPNM), which derives context-specific PINs in real-time
from the PubMed database based on a set of user-input keywords and
enhanced PubMed query system. CPNM reports enriched information on
protein interactions (with type and directionality), their network
topology with summary statistics (e.g. most densely connected proteins
in the network; most densely connected protein-pairs; and proteins
connected by most inbound/outbound links) that can be explored via a
user-friendly interface. Some of the novel features of the CPNM system
include PIN generation, ontology-based PubMed query enhancement,
real-time, user-queried, up-to-date PubMed document processing, and
prediction of PIN directionality.
Conclusions
CPNM provides a tool for biologists to explore PINs.