BioCompass: A Novel Functional Inference Tool that Utilizes MeSH Hierarchy to Analyze Groups of Genes

• Published in: In silico biology Vol. 8; no. 1; pp. 53 - 61
• Main Authors: Nakazato, Takeru, Takinaka, Toru, Mizuguchi, Hironori, Matsuda, Hideo, Bono, Hidemasa, Asogawa, Minoru
• Format: Journal Article
• Language: English
• Published: London, England SAGE Publications 2008; IOS Press
• Subjects: Biological and medical sciences; Computational Biology; Databases, Genetic; Fundamental and applied biological sciences. Psychology; General aspects; Genes; Information Storage and Retrieval - methods; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Medical Subject Headings; MEDLINE; Software; User-Computer Interface; MEDLINE; MeSH terms; microarray; OMIM; text mining; machine learning; Gene Ontology; Text mining; Gene ontology; Data analysis; Experimental data; Gene; Machine learning; Software; Microarray; Bioinformatics
• ISSN: 1386-6338; 1434-3207
• DOI: 10.3233/ISB-00343

Microarray technology has become employed widely for biological researchers to identify genes associated with conditions such as diseases and drugs. To date, many methods have been developed to analyze data covering a large number of genes, but they focus only on statistical significance and cannot decipher the data with biological concepts. Gene Ontology (GO) is utilized to understand the data with biological interpretation; however, it is restricted to specific ontology such as biological process, molecular function, and cellular component. Here, we attempted to apply MeSH (Medical Subject Headings) to interpret groups of genes from biological viewpoint. To assign MeSH terms to genes, in this study, contexts associated with genes are retrieved from full set of MEDLINE data using machine learning, and then extracted MeSH terms from retrieved articles. Utilizing the developed method, we implemented a software called BioCompass. It generates high-scoring lists and hierarchical lists for diseases MeSH terms associated with groups of genes to utilize MeSH and GO tree, and illustrated a wiring diagram by linking genes with extracted association from articles. Researchers can easily retrieve genes and keywords of interest, such as diseases and drugs, associated with groups of genes. Using retrieved MeSH terms and OMIM in conjunction with, we could obtain more disease information associated with target gene. BioCompass helps researchers to interpret groups of genes such as microarray data from a biological viewpoint.