geWorkbench

Revision as of 18:34, 13 August 2008

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

A new ARACNE tutorial is coming soon....

ARACNE in geWorkbench is used to determine interactions between a hub gene and a set of selected genes (or all genes in the set).

The resulting adjancency matrix will be displayed in the Cytoscape network visualization component.

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 ==Quick Example==
-# Load a microarray dataset, e.g. "webmatrix2_quantile_log2_dev1.2_mv0.exp" (2226 probes).
+# Load a microarray dataset, e.g. Bcell-100.exp.
 # Set a hub gene (e.g 1973_s_at)
 # Click Analyze.
 The resulting adjancency matrix will be displayed in the Cytoscape network visualization component.