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. 2012;7(4):e34480.
doi: 10.1371/journal.pone.0034480. Epub 2012 Apr 6.

Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature

Rajesh Chowdhary  1 , Sin Lam Tan, Jinfeng Zhang, Shreyas Karnik, Vladimir B Bajic, Jun S Liu
Affiliations

Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature

Rajesh Chowdhary et al. PLoS One. 2012.

Abstract

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/.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Architecture of CPNM system.
Figure 2
Figure 2. CPNM web interface with query builder.
Figure 3
Figure 3. Sample query formulation by CPNM.
Figure 4
Figure 4. CPNM output showing protein interactions extracted from literature for Case Study I.
Figure 5
Figure 5. PIN generated by CPNM for Case Study I.
Figure 6
Figure 6. PIN generated by CPNM for Case Study II.
Figure 7
Figure 7. Hub nodes in PIN generated by CPNM for Case Study II.
See this image and copyright information in PMC

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