GAGE Web

Generally Applicable Gene-set/Pathway Analysis

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Overview (current)
GAGE Analysis
Example Analysis1
Example Analysis2
Example Analysis3
Discrete Gage Analysis
Instructions

Example GAGE Analysis 2: Gene Data with Custom Gene Sets

Input / Output
Analysis
Pathview

Graphics
Pathview

Coloration

Assay Data:

gse16873.symb.txt

Data

Control/Refernce

Case/Sample

Note: Ctrl-click to unselect

Compare:

Log transformed:

Count data:

Normalized data:

Data Type:

Species:

Gene Set:

c1_all_v3_0_symbols.gmt

Note: Ctrl-click to unselect

Gene ID Type:

(Gene / Compound)

q-value Cutoff:

Set Size, Minimum:

Maximum:

Two-direction Test:

Rank Test:

Per Gene Score:

Gene Set Test:

Use Pathview:

Pathview Settings:

Kegg Native:

Same Layer:

Descrete Gene:

Descrete Compound:

Multi State:

Match Data:

Compound Label Offset:

Key Alignment:

Signature Position:

Key

Position:

Node Sum:

NA Color:

Attribute

Gene Compound

Limit:

Bins:

Low:

Mid:

High:

Signaling & Metabolic
Signaling
Metabolic
Disease
All
Biological Process
Cellular Component
Molecular Function
All
Custom

Note: Ctrl-click to unselect

Maximum:

Key

Position:

Bioinformatics Services Division - Department of Bioinformatics and Genomics - UNC Charlotte