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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Context-specific protein network miner - an online system for exploring context-specific protein interaction networks from the literature
PLoS ONE, Volume 7, No. 4, Article e34480, Year 2012
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Description
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. It is freely accessible at http://www.biotextminer.com/CPNM/. © 2012 Chowdhary et al.
Authors & Co-Authors
Chowdhary, Rajesh
United States, Marshfield
Marshfield Clinic
Tan, Sinlam
United States, Marshfield
Marshfield Clinic
Zhang, Jinfeng
United States, Tallahassee
Florida State University
Karnik, Shreyas
United States, Marshfield
Marshfield Clinic
Bajic, Vladimir B.
Saudi Arabia, Thuwal
King Abdullah University of Science and Technology
Liu, Jun S.
United States, Cambridge
Harvard University
Statistics
Citations: 21
Authors: 6
Affiliations: 4
Identifiers
Doi:
10.1371/journal.pone.0034480
e-ISSN:
19326203
Study Design
Exploratory Study