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Related Experiment Videos

CoPub Mapper: mining MEDLINE based on search term co-publication.

Blaise T F Alako1, Antoine Veldhoven, Sjozef van Baal

  • 1Department of Molecular Design & Informatics, Organon NV, P.O. Box 20, 5340 BH Oss, The Netherlands. blaise.alako@wur.nl

BMC Bioinformatics
|March 12, 2005
PubMed
Summary

This study introduces CoPub Mapper, a tool that analyzes gene co-mentions in scientific literature to identify biological similarities and cluster genes effectively, aiding in the interpretation of microarray data.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • High-throughput microarray analyses yield numerous differentially expressed genes requiring biological interpretation.
  • Identifying biological similarities between genes is crucial for understanding complex biological processes.
  • Literature co-mentions offer a valuable resource for inferring gene relationships.

Purpose of the Study:

  • To develop and validate a program for identifying biological similarities between genes using literature co-mentions.
  • To assess the program's ability to cluster genes based on co-publication patterns.
  • To apply the program to real microarray data for biological process and disease keyword discovery.

Main Methods:

  • Generated and validated MEDLINE search strings for 15,621 genes and 3,731 keywords.

Related Experiment Videos

  • Retrieved PubMed IDs and calculated co-occurrence probabilities for gene-gene and gene-keyword pairs.
  • Utilized Receiver Operator Characteristics (ROC) analyses to evaluate gene clustering accuracy.
  • Applied hierarchical clustering to group genes and keywords based on co-occurrence.

    • Main Results:

    • The program successfully clustered predefined gene sets with known biological connections, outperforming random chance.
    • Analysis of 221 differentially expressed genes from microarray data revealed relevant gene clusters associated with biological processes and diseases.
    • Hierarchical clustering provided a comprehensive grouping of published genes based on literature co-occurrence.

    Conclusions:

    • CoPub Mapper offers a rapid and flexible method for querying co-published genes and keywords.
    • The program effectively clusters predefined gene groups and microarray data, facilitating biological interpretation.