GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms.

Marcel Smid; Lambert C J Dorssers

doi:10.1093/bioinformatics/bth293

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GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms.

Marcel Smid·Lambert C J Dorssers

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Abstract

MOTIVATION: Retrieval of information on biological processes from large-scale expression data is still a time-consuming task. An automated analysis utilizing all expression information would greatly increase our understanding of the samples under study. RESULTS: We describe here a novel method to obtain a functional analysis of complex gene expression data. Instead of applying a predefined expression threshold, Gene Ontology (GO) terms are weighted using the actual measured levels of expression of all associated genes. Based on this concept, the application GO-Mapper was developed to quantitatively link gene expression levels to GO-terms for multiple experiments in an automated way. The applicability of GO-Mapper was developed and validated on in house and public human microarray data and mouse SAGE data. We demonstrate that the GO-Mapper allows for interrelating relevant biological functions with the experiments under study. AVAILABILITY: The GO-Mapper application is free of charge available from our website.

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Algorithms Animals Databases, Protein Documentation Gene Expression Profiling Humans Mice Natural Language Processing Oligonucleotide Array Sequence Analysis Proteins Software Structure-Activity Relationship User-Computer Interface Comparative Study Evaluation Study Journal Article Research Support, Non-U.S. Gov't Validation Study

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Marcel Smid, Lambert C J Dorssers. 2004-05-06. GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms.. https://doi.org/10.1093/bioinformatics%2Fbth293

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