Expander 5.2 Online Documentation

Table of Contents

Expander 5.2 Online Documentation. 1

Introduction. 1

Starting EXPANDER.. 2

Input Data. 3

Tabular Data File. 3

CEL Files. 5

Working on Gene Groups with no associated expression data. 7

Preprocessing GE Data. 9

Viewing Data Plots. 13

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

Biclustering GE Data. 20

Network Based Grouping of GE Data. 25

Group Analysis Tools. 27

Functional Analysis. 27

Promoter Analysis. 31

Location Enrichment Analysis. 35

miRNA Targets Enrichment Analysis. 39

Pathway Enrichment Analysis. 43

General Enrichment Analysis. 43

Network Based Group Analysis. 46

Matrix Visualizations. 47

Hierarchical Clustering and Visualization. 49

PCA Transformation. 51

Analysis Wizard. 51

Additional Options. 52

File Formats. 55

Sample Input Files. 58

Supplied Files. 58

Settings. 64

R External Application. 65

FAQ.. 66

Copyrights Information. 69

References. 70

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
• Biclustering GE Data
• Network Based Grouping of GE Data
• Group Analysis Tools
•  
• Matrix Visualizations
• Hierarchical Clustering and Visualization
• PCA Transformation
•  
• Analysis Wizard
• Additional Options
• File Formats
• Sample Input Files
• Supplied Files
• Settings
• R External Application
• FAQ
• Copyrights Information
• References