Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data. Export

@article{citeulike:809434, abstract = {MOTIVATION: Today, the characterization of clinical phenotypes by gene-expression patterns is widely used in clinical research. If the investigated phenotype is complex from the molecular point of view, new challenges arise and these have not been addressed systematically. For instance, the same clinical phenotype can be caused by various molecular disorders, such that one observes different characteristic expression patterns in different patients. RESULTS: In this paper we describe a novel algorithm called Structured Analysis of Microarrays (StAM), which accounts for molecular heterogeneity of complex clinical phenotypes. Our algorithm goes beyond established methodology in several aspects: in addition to the expression data, it exploits functional annotations from the Gene Ontology database to build biologically focussed classifiers. These are used to uncover potential molecular disease subentities and associate them to biological processes without compromising overall prediction accuracy. AVAILABILITY: Bioconductor compliant R package SUPPLEMENTARY INFORMATION: Complete analyses are available at http://compdiag.molgen.mpg.de/supplements/lottaz05.}, address = {Max Planck Institute for Molecular Genetics and Berlin Center for Genome Based Bioinformatics, Germany. Claudio.Lottaz@molgen.mpg.de}, author = {Lottaz, Claudio and Spang, Rainer}, citeulike-article-id = {809434}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/bti292}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/15677704}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=15677704}, day = {1}, doi = {10.1093/bioinformatics/bti292}, issn = {1367-4803}, journal = {Bioinformatics (Oxford, England)}, keywords = {classification, geneset, go, microarray}, month = {May}, number = {9}, pages = {1971--1978}, posted-at = {2009-01-29 16:05:58}, priority = {2}, title = {Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data.}, url = {http://dx.doi.org/10.1093/bioinformatics/bti292}, volume = {21}, year = {2005} }

TY - JOUR ID - citeulike:809434 L3 - citeulike-article-id:809434 N2 - MOTIVATION: Today, the characterization of clinical phenotypes by gene-expression patterns is widely used in clinical research. If the investigated phenotype is complex from the molecular point of view, new challenges arise and these have not been addressed systematically. For instance, the same clinical phenotype can be caused by various molecular disorders, such that one observes different characteristic expression patterns in different patients. RESULTS: In this paper we describe a novel algorithm called Structured Analysis of Microarrays (StAM), which accounts for molecular heterogeneity of complex clinical phenotypes. Our algorithm goes beyond established methodology in several aspects: in addition to the expression data, it exploits functional annotations from the Gene Ontology database to build biologically focussed classifiers. These are used to uncover potential molecular disease subentities and associate them to biological processes without compromising overall prediction accuracy. AVAILABILITY: Bioconductor compliant R package SUPPLEMENTARY INFORMATION: Complete analyses are available at http://compdiag.molgen.mpg.de/supplements/lottaz05. IS - 9 JF - Bioinformatics (Oxford, England) SN - 1367-4803 AD - Max Planck Institute for Molecular Genetics and Berlin Center for Genome Based Bioinformatics, Germany. Claudio.Lottaz@molgen.mpg.de EP - 1978 TI - Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data. VL - 21 SP - 1971 KW - classification KW - geneset KW - go KW - microarray AU - Lottaz, Claudio AU - Spang, Rainer PY - 2005/05/01/ UR - http://dx.doi.org/10.1093/bioinformatics/bti292 ER -