input data for analysis
DESCRIPTION
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 PresentationTRANSCRIPT
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Input data for analysis
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Users that have expression values (dataset 1_ chicken affy_foldchane.txt.can upload that file as shown in slide 30
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Input data format
More information available in IPA_workshop.doc
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Save input data as a new project including metadata
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Create analysis
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Analysis settingsApplying filters
Information about mapped/unmapped data
More information available in IPA_workshop.doc
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Unmapped IDs
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Mapped Ids
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Run Analysis
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Progress of analysis
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Analysis summary
Export
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Networks tab of analysis
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Select and view network
Right click
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Top network
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Functions tab
Biological functions
More information available in IPA_workshop.doc
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Customize functions
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Molecular and cellular functions only
Export options
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Export functions
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Navigate the functions displayed as a DAG
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Canonical pathways
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Customize pathways
Statistical scoring
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Signaling pathways
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Coverage i.e. ratioOf pathways
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Entities in the pathway
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TREM1 signaling pathway
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TREM1 signaling pathway
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Data input with fold change
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Data input with fold change
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Networks tab. Genes have associated fold change(decrease (green) and increase (red))
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Top network with fold change
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TREM1 signaling
Some IPA results are available in the folder entitledIPA_results
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TREM1 signaling
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Search analysis results
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Results of search for ‘invasion’
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Creating lists from Functions tab
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Select a set of genes and save as ‘new list’
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Selected lists can be exported to additional tools
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List exported as a ‘new pathway’
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Connect all entities in the list
Select all entities
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Build connections
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Build connections applying all desired filters
More information available in IPA_workshop.doc
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Interconnected genes from the list
Save as a new pathway
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Saved list& pathway
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Overlay expression values to the new pathway
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Select analyzed dataset
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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