Input data for analysis

Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Input data format More information available in IPA_workshop.doc

Save input data as a new project including metadata

Create analysis

Analysis settings Applying filters Information about mapped/unmapped data More information available in IPA_workshop.doc

Unmapped IDs

Mapped Ids

Run Analysis

Progress of analysis

Analysis summary Export

Networks tab of analysis

Select and view network Right click

Top network

Functions tab Biological functions More information available in IPA_workshop.doc

Customize functions

Molecular and cellular functions only Export options

Export functions

Navigate the functions displayed as a DAG

Canonical pathways

Customize pathways Statistical scoring

Signaling pathways

Coverage i.e. ratio Of pathways

Entities in the pathway

TREM1 signaling pathway

Data input with fold change

Networks tab. Genes have associated fold change (decrease (green) and increase (red))

Top network with fold change

TREM1 signaling Some IPA results are available in the folder entitled IPA_results

TREM1 signaling

Search analysis results

Results of search for ‘invasion’

Creating lists from Functions tab

Select a set of genes and save as ‘new list’

Selected lists can be exported to additional tools

List exported as a ‘new pathway’

Connect all entities in the list Select all entities

Build connections

Build connections applying all desired filters More information available in IPA_workshop.doc

Interconnected genes from the list Save as a new pathway

Saved list & pathway

Overlay expression values to the new pathway

Select analyzed dataset

Acknowledgement Ingenuity Pathways Analysis (web and help manual) IPA offers weekly (Thursday) training Additional IPA resources