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Input data for analysis. Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30. More information available in IPA_workshop.doc. Input data format. Save input data as a new project including metadata. Create analysis. - PowerPoint PPT Presentation
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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