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Comprehensive Guide to Analyzing Chicken Gene Expression Data Using IPA

This guide provides step-by-step instructions for analyzing chicken gene expression data using the Ingenuity Pathway Analysis (IPA) software. It covers uploading expression values, creating new projects with metadata, applying filters, and interpreting mapped/unmapped data. Detailed instructions on running analyses, exporting networks, and customizing biological functions are included. Also discussed are TREM1 signaling pathways, statistical scoring, and how to build connections between interrelated genes. For further resources, refer to the IPA workshop documentation and training links.

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Comprehensive Guide to Analyzing Chicken Gene Expression Data Using IPA

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  1. Input data for analysis

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

  3. More information available in IPA_workshop.doc Input data format

  4. Save input data as a new project including metadata

  5. Create analysis

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

  7. Unmapped IDs

  8. Mapped Ids

  9. Run Analysis

  10. Progress of analysis

  11. Analysis summary Export

  12. Networks tab of analysis

  13. Select and view network Right click

  14. Top network

  15. Functions tab More information available in IPA_workshop.doc Biological functions

  16. Customize functions

  17. Molecular and cellular functions only Export options

  18. Export functions

  19. Navigate the functions displayed as a DAG

  20. Canonical pathways

  21. Customize pathways Statistical scoring

  22. Signaling pathways

  23. Coverage i.e. ratio Of pathways

  24. Entities in the pathway

  25. TREM1 signaling pathway

  26. TREM1 signaling pathway

  27. Data input with fold change

  28. Data input with fold change

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

  30. Top network with fold change

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

  32. TREM1 signaling

  33. Search analysis results

  34. Results of search for ‘invasion’

  35. Creating lists from Functions tab

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

  37. Selected lists can be exported to additional tools

  38. List exported as a ‘new pathway’

  39. Connect all entities in the list Select all entities

  40. Build connections

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

  42. Interconnected genes from the list Save as a new pathway

  43. Saved list & pathway

  44. Overlay expression values to the new pathway

  45. Select analyzed dataset

  46. Acknowledgement Ingenuity Pathways Analysis (web and help manual) IPA offers weekly (Thursday) training http://www.ingenuity.com/products/training.html Additional IPA resources http://www.ingenuity.com/library/index.html

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