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Introduction. 2
Starting EXPANDER.. 2
Input Data. 3
Tabular Data File. 4
CEL Files. 6
Working on similarity data no associated expression
data. 9
Working on Gene Groups with no associated expression
data. 10
ChIP-Seq Data. 12
Preprocessing GE Data. 15
Gene Expression Data Plots. 20
Differential Expression Analysis. 21
Defining a group according to a rule. 23
Defining a group according to similarity
to a selected probe. 24
Clustering GE Data. 24
Hierarchical Clustering and
Visualization. 28
Clustering solution cleaning. 30
Biclustering GE Data. 31
Network Based Grouping of GE Data. 36
Integrative analysis of ChIP-Seq and
Gene Expression Data. 40
Group Enrichments Analysis Tools. 42
Functional Analysis. 43
Promoter Analysis. 46
Location Enrichment Analysis. 54
miRNA Targets Enrichment Analysis. 59
ChIP-Seq Enrichment Analysis. 63
Pathway Enrichment Analysis. 66
General Enrichment Analysis. 69
Network Based Enrichment Analysis. 73
Gene Set Enrichment Analysis (GSEA). 74
Matrix Visualizations. 81
PCA Transformation. 82
Analysis Wizard. 83
Additional Options. 84
File Formats. 87
Sample Input Files. 91
Supplied Files. 92
Settings. 97
R External Application. 98
Manually installation of R packages. 99
FAQ.. 100
Copyrights Information. 105
References. 106
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