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 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 settingsApplying 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. ratioOf pathways

Entities in the pathway

TREM1 signaling pathway

TREM1 signaling pathway

Data input with fold change

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 entitledIPA_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) traininghttp://www.ingenuity.com/products/training.html

Additional IPA resources http://www.ingenuity.com/library/index.html