geWorkbench

Revision as of 15:56, 14 January 2014

Home \| Quick Start \| Basics \| Menu Bar \| Preferences \| Component Configuration Manager \| Workspace \| Information Panel \| Local Data Files \| File Formats \| caArray \| Array Sets \| Marker Sets \| Microarray Dataset Viewers \| Filtering \| Normalization \| Tutorial Data \| geWorkbench-web Tutorials	Analysis Framework \| ANOVA \| ARACNe \| BLAST \| Cellular Networks KnowledgeBase \| CeRNA/Hermes Query \| Classification (KNN, WV) \| Color Mosaic \| Consensus Clustering \| Cytoscape \| Cupid \| DeMAND \| Expression Value Distribution \| Fold-Change \| Gene Ontology Term Analysis \| Gene Ontology Viewer \| GenomeSpace \| genSpace \| Grid Services \| GSEA \| Hierarchical Clustering \| IDEA \| Jmol \| K-Means Clustering \| LINCS Query \| Marker Annotations \| MarkUs \| Master Regulator Analysis \| (MRA-FET Method) \| (MRA-MARINa Method) \| MatrixREDUCE \| MINDy \| Pattern Discovery \| PCA \| Promoter Analysis \| Pudge \| SAM \| Sequence Retriever \| SkyBase \| SkyLine \| SOM \| SVM \| T-Test \| Viper Analysis \| Volcano Plot

Coming soon!

The "GSEA Analysis" and "GSEA Browser" must be loaded in the Component Configuration Manager.

Two (and only two) array sets must be activated in the Arrays component. They do not need to be marked "Case" or "Control", this will have no effect. These sets define the two classes used to calculate a measure of differential expression and from that the rank order of genes.

Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 102(43):15545-50. PubMed 16199517

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 ==References==
-Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.  Proc Natl Acad Sci U S A. 102(43):15545-50. [http://www.ncbi.nlm.nih.gov/pubmed/16199517 PubMed 16199517]
+* Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.  Proc Natl Acad Sci U S A. 102(43):15545-50. [http://www.ncbi.nlm.nih.gov/pubmed/16199517 PubMed 16199517]
-GenePattern [http://www.broadinstitute.org/cancer/software/genepattern/modules modules] documentation.
+* GenePattern [http://www.broadinstitute.org/cancer/software/genepattern/modules modules] documentation.
-[http://www.broadinstitute.org/cancer/software/genepattern/modules/docs/GSEA/14 GSEA v14] online documentation.
+* [http://www.broadinstitute.org/cancer/software/genepattern/modules/docs/GSEA/14 GSEA v14] online documentation.