Global Mapping of Gene/Protein Interactions in PubMed Abstracts: A Framework and an Experiment with P53 Interactions

Abstract

Gene/protein interactions provide critical information for a thorough understanding of cellular processes. Recently, considerable interest and effort has been focused on the construction and analysis of genome-wide gene networks. The large body of biomedical literature is an important source of gene/protein interaction information. Recent advances in text mining tools have made it possible to automatically extract such documented interactions from free-text literature. In this paper, we propose a comprehensive framework for constructing and analyzing large-scale gene functional networks based on the gene/protein interactions extracted from biomedical literature repositories using text mining tools. Our proposed framework consists of analyses of the network topology, network topology-gene function relationship, and temporal network evolution to distill valuable information embedded in the gene functional interactions in literature. We demonstrate the application of the proposed framework using a testbed of P53-related PubMed abstracts, which shows that literature-based P53 networks exhibit small-world and scale-free properties. We also found that high degree genes in the literature-based networks have a high probability of appearing in the manually curated database and genes in the same pathway tend to form local clusters in our literature-based networks. Temporal analysis showed that genes interacting with many other genes tend to be involved in a large number of newly discovered interactions.

References in corpus (13)

• Emergence of scaling in random networks
• Statistical mechanics of complex networks
• Finding and evaluating community structure in networks
• Modularity and community structure in networks
• Lethality and centrality in protein networks
• Hierarchical organization of modularity in metabolic networks
• The large-scale organization of metabolic networks
• Random graphs with arbitrary degree distributions and their applications
• Evolution of the social network of scientific collaborations
• How Popular is Your Paper? An Empirical Study of the Citation Distribution
• Measuring preferential attachment for evolving networks
• The topology of the transcription regulatory network in the yeast, S. cerevisiae
• Topological Properties of Citation and Metabolic Networks

Cited by in corpus (2)

• Gene Function Prediction with Gene Interaction Networks: A Context Graph Kernel Approach
• Filtering Microarray Correlations by Statistical Literature Analysis Yields Potential Hypotheses for Lactation Research