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


BACKGROUND
The GO-Mapper application is free of charge available from our website.
Smid
Marcel
M
Department of Pathology, Josephine Nefkens Institute, Erasmus MC, P.O. Box 1738, 3000DR Rotterdam, The Netherlands.
Dorssers
Lambert C J
LC
D000465:Algorithms; D000818:Animals; D030562:Databases, Protein; D004282:Documentation / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D051379:Mice; D009323:Natural Language Processing; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000145:classification / Q000378:metabolism*; D012984:Software; D013329:Structure-Activity Relationship; D014584:User-Computer Interface
D011506:Proteins