Ingenuity Pathway Analysis (IPA) Training

Tufts University Users should follows these instructions to set up their IPA account before attending the workshop:

https://it.tufts.edu/research-technology/bioinformatics/ingenuity-pathway-analysis

Part I: Navigating the IPA knowledgebase (BKB): Query and visualize molecular-phenotypic interactions 

• Overview of the Biomedical Knowledge Base
• Generate a network for genes, chemicals and diseases 
  • Activity prediction for hypothesis generation and experiment design
  • Project searching

Part II: Core Analysis of user Omics data (gene/transcript/protein or metabolite)

• Preparing your data for upload
  • Dataset and file formats
  • Settings and options for configuring a core analysis
• Paradigms for data reduction and biological interpretation in the core analysis
  • Biological mechanisms, regulators and targets
  • Compare across groups (time points, treatments, sc clusters etc.)
  • Activity heatmap for pathways, regulators and bio functions
  • Compare contrast activity of pathways, bio. functions and regulators
  • Discover condition-specific biomarkers 
• Functional comparisons of user data with published data
  • Analysis Match, activity plot, patter search
  • Heatmaps, hierarchical clustering

Part III: Surveillance of Public Data with Land Explorer

• (GEO, SRA, TCGA etc.) 
  • Investigate a gene/biomarker’s expression across diseases, tissues, cell types etc.
  • Derive gene/biomarker signatures for condition of interest (ex. treatment, disease subtype, cell type etc.)
• Searching and interpretation of published expression analyses
  • Search and open pathway analyses of public datasets
  • Study biological mechanisms and discover key regulators/drug targets