Expander 6.4 Online Documentation

Introduction. 1

Starting EXPANDER.. 2

Input Data. 3

Tabular Data File. 3

CEL Files. 5

Working on similarity data no associated expression data. 7

Working on Gene Groups with no associated expression data. 8

Preprocessing GE Data. 10

Viewing Data Plots. 14

Differential Expression Analysis. 15

Defining a group according to a rule. 16

Defining a group according to similarity to a selected probe. 17

Clustering GE Data. 17

Hierarchical Clustering and Visualization. 20

Biclustering GE Data. 22

Network Based Grouping of GE Data. 27

Group Enrichments Analysis Tools. 30

Functional Analysis. 30

Promoter Analysis. 34

Location Enrichment Analysis. 41

miRNA Targets Enrichment Analysis. 44

Pathway Enrichment Analysis. 48

General Enrichment Analysis. 53

Network Based Enrichment Analysis. 56

Gene Set Enrichment Analysis (GSEA) 57

Matrix Visualizations. 61

PCA Transformation. 62

Analysis Wizard. 63

Additional Options. 64

File Formats. 66

Sample Input Files. 69

Supplied Files. 69

Settings. 74

R External Application. 75

Manually installation of R packages. 76

FAQ.. 76

Copyrights Information. 80

References. 81

Table of Contents

• Introduction
• Starting EXPANDER
• Input Data
• Preprocessing GE Data
• Viewing Data Plots
• Differential Expression Analysis
• Defining a group according to a rule
• Defining a group according to similarity to a selected probe
• Clustering GE Data
• Hierarchical Clustering and Visualization
• Biclustering GE Data
• Network Based Grouping of GE Data
• Group  Enrichments Analysis Tools
• Matrix Visualizations
• PCA Transformation
• Analysis Wizard
• Additional Options
• File Formats
• Sample Input Files
• Supplied Files
• Settings
• R External Application
• FAQ
• Copyrights Information
• References