Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
1
pubmed:dateCreated
2009-2-2
pubmed:abstractText
Gene-set analysis aims to identify differentially expressed gene sets (pathways) by a phenotype in DNA microarray studies. We review here important methodological aspects of gene-set analysis and illustrate them with varying performance of several methods proposed in the literature. We emphasize the importance of distinguishing between 'self-contained' versus 'competitive' methods, following Goeman and Bühlmann. We also discuss reducing a gene set to its subset, consisting of 'core members' that chiefly contribute to the statistical significance of the differential expression of the initial gene set by phenotype. Significance analysis of microarray for gene-set reduction (SAM-GSR) can be used for an analytical reduction of gene sets to their core subsets. We apply SAM-GSR on a microarray dataset for identifying biological gene sets (pathways) whose gene expressions are associated with p53 mutation in cancer cell lines. Codes to implement SAM-GSR in the statistical package R can be downloaded from http://www.ualberta.ca/~yyasui/homepage.html.
pubmed:grant
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-11309499, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-12064478, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-12620386, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-12808457, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-14663481, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-14693814, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-15152076, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-15647293, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-15657105, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-16113772, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-16174746, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-16199517, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-16585533, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-16651662, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-16877751, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-17118132, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-17127676, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-17303618, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-17553853, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-17612399, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-17988400, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-18202032, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-18331198, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-9363941, http://linkedlifedata.com/resource/pubmed/commentcorrection/18836208-9841917
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jan
pubmed:issn
1477-4054
pubmed:author
pubmed:issnType
Electronic
pubmed:volume
10
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
24-34
pubmed:dateRevised
2010-9-21
pubmed:meshHeading
pubmed:year
2009
pubmed:articleTitle
Gene-set analysis and reduction.
pubmed:affiliation
PhD, School of Public Health, University of Alberta, 13-106J Clinical Sciences Building, Edmonton, Alberta T6G2G3, Canada. idinu@ualberta.ca
pubmed:publicationType
Journal Article, Review, Research Support, Non-U.S. Gov't, Research Support, N.I.H., Extramural