input data for analysis users that have expression values (dataset 1_ chicken affy_foldchane.txt....

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Page 1: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30
Page 2: 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

Page 3: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30
Page 4: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

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

Page 5: 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

Page 6: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Save input data as a new project including metadata

Page 7: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Create analysis

Page 8: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Analysis settingsApplying filters

Information about mapped/unmapped data

More information available in IPA_workshop.doc

Page 9: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Unmapped IDs

Page 10: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Mapped Ids

Page 11: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Run Analysis

Page 12: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Progress of analysis

Page 13: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Analysis summary

Export

Page 14: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Networks tab of analysis

Page 15: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Select and view network

Right click

Page 16: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Top network

Page 17: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Functions tab

Biological functions

More information available in IPA_workshop.doc

Page 18: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Customize functions

Page 19: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Molecular and cellular functions only

Export options

Page 20: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Export functions

Page 21: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Navigate the functions displayed as a DAG

Page 22: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Canonical pathways

Page 23: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Customize pathways

Statistical scoring

Page 24: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Signaling pathways

Page 25: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Coverage i.e. ratioOf pathways

Page 26: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Entities in the pathway

Page 27: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

TREM1 signaling pathway

Page 28: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

TREM1 signaling pathway

Page 29: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Data input with fold change

Page 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

Data input with fold change

Page 31: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

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

Page 32: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Top network with fold change

Page 33: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

TREM1 signaling

Some IPA results are available in the folder entitledIPA_results

Page 34: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

TREM1 signaling

Page 35: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Search analysis results

Page 36: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Results of search for ‘invasion’

Page 37: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Creating lists from Functions tab

Page 38: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

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

Page 39: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30
Page 40: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Selected lists can be exported to additional tools

Page 41: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

List exported as a ‘new pathway’

Page 42: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Connect all entities in the list

Select all entities

Page 43: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Build connections

Page 44: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Build connections applying all desired filters

More information available in IPA_workshop.doc

Page 45: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Interconnected genes from the list

Save as a new pathway

Page 46: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Saved list& pathway

Page 47: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Overlay expression values to the new pathway

Page 48: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

Select analyzed dataset

Page 49: Input data for analysis Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

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