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Table of Contents
Introduction. 1
Starting EXPANDER.. 1
Input Data. 3
Tabular Data File. 3
CEL Files. 5
Gene Sets: 8
Preprocessing GE Data. 9
Viewing Data Plots. 14
Clustering GE Data. 16
Biclustering GE Data. 19
Network Based Grouping of GE Data. 24
Group Analysis Tools. 26
Functional Analysis. 26
Promoter Analysis. 30
Location Enrichment Analysis. 34
miRNA Targets Enrichment Analysis. 38
General Enrichment Analysis. 42
Network Based Group Analysis. 45
Matrix Visualizations (Heat maps) 46
Hierarchical Clustering and
Visualization. 47
PCA Transformation. 49
Additional Options. 49
File Formats. 52
Sample Input Files. 54
Supplied Files. 55
Settings. 61
R External Application. 62
FAQ.. 63
Copyrights Information. 66
References. 67
Table of Contents
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