A global test for groups of genes: testing association with a clinical outcome. Export

@article{citeulike:1155486, abstract = {MOTIVATION: This paper presents a global test to be used for the analysis of microarray data. Using this test it can be determined whether the global expression pattern of a group of genes is significantly related to some clinical outcome of interest. Groups of genes may be any size from a single gene to all genes on the chip (e.g. known pathways, specific areas of the genome or clusters from a cluster analysis). RESULT: The test allows groups of genes of different size to be compared, because the test gives one p-value for the group, not a p-value for each gene. Researchers can use the test to investigate hypotheses based on theory or past research or to mine gene ontology databases for interesting pathways. Multiple testing problems do not occur unless many groups are tested. Special attention is given to visualizations of the test result, focussing on the associations between samples and showing the impact of individual genes on the test result. AVAILABILITY: An R-package globaltest is available from http://www.bioconductor.org}, address = {Department of Medical Statistics, Leiden University Medical Center, P.O. Box 9604, 2300 RC Leiden, The Netherlands. j.j.goeman@lumc.nl}, author = {Goeman, Jelle J. and van de Geer, Sara A. and de Kort, Floor and van Houwelingen, Hans C.}, citeulike-article-id = {1155486}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btg382}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/1/93}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/14693814}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=14693814}, day = {1}, doi = {10.1093/bioinformatics/btg382}, issn = {1367-4803}, journal = {Bioinformatics (Oxford, England)}, keywords = {bioconductor, globaltest, gsea, r, r-package}, month = {January}, number = {1}, pages = {93--99}, posted-at = {2009-02-23 16:01:01}, priority = {2}, title = {A global test for groups of genes: testing association with a clinical outcome.}, url = {http://dx.doi.org/10.1093/bioinformatics/btg382}, volume = {20}, year = {2004} }

TY - JOUR ID - citeulike:1155486 L3 - citeulike-article-id:1155486 N2 - MOTIVATION: This paper presents a global test to be used for the analysis of microarray data. Using this test it can be determined whether the global expression pattern of a group of genes is significantly related to some clinical outcome of interest. Groups of genes may be any size from a single gene to all genes on the chip (e.g. known pathways, specific areas of the genome or clusters from a cluster analysis). RESULT: The test allows groups of genes of different size to be compared, because the test gives one p-value for the group, not a p-value for each gene. Researchers can use the test to investigate hypotheses based on theory or past research or to mine gene ontology databases for interesting pathways. Multiple testing problems do not occur unless many groups are tested. Special attention is given to visualizations of the test result, focussing on the associations between samples and showing the impact of individual genes on the test result. AVAILABILITY: An R-package globaltest is available from http://www.bioconductor.org IS - 1 JF - Bioinformatics (Oxford, England) SN - 1367-4803 AD - Department of Medical Statistics, Leiden University Medical Center, P.O. Box 9604, 2300 RC Leiden, The Netherlands. j.j.goeman@lumc.nl EP - 99 TI - A global test for groups of genes: testing association with a clinical outcome. VL - 20 SP - 93 KW - bioconductor KW - globaltest KW - gsea KW - r KW - r-package AU - Goeman, Jelle AU - van de Geer, Sara AU - de Kort, Floor AU - van Houwelingen, Hans PY - 2004/01/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btg382 ER -