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Tools and Algorithms in Bioinformatics
GCBA815, Fall 2015
Week-10: IPA: Ingenuity Pathway Analysis
Babu Guda
Department of Genetics, Cell Biology and Anatomy
University of Nebraska Medical Center
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Ingenuity Pathway Analysis (IPA)
http://www.ingenuity.com
•  A leading commercial software for biological pathway and network
analysis
•  Ingenuity knowledge Base (expert curated information from the
literature)
•  Public databases (Entrez Gene, RefSeq, OMIM, GWAS, GO,
HMDB, GNF, KEGG, IntAct, BIND, Clinical trials, DrugBank, etc.)
•  Four major products
•  IPA (UNMC has two concurrent licenses)
•  iReport: Interactive web-based report
•  Variant Analysis: To identify variants from sequencing data
•  BioProfiler: Profiles a disease or phenotype by associating
genes and compounds
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Different types of analyses
•  Browsing the database (genes, molecules, diseases, pathways and
functions using the IPA knowledgebase)
•  Gene expression analysis
•  Pathway analysis (signaling, metabolic, disease)
•  Interaction network analysis
•  Grow/build networks from seed molecules
•  Trim larger networks
•  Upstream regulator analysis
•  Mechanistic network analysis
•  Human Isoform view
•  Molecule activity predictor (MAP)
•  Predicted cascading effects of altering one molecule in a pathway
•  Hypothesis generation
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Some special features of IPA
•  Search feature against the entire IPA Knowledgebase
•  Molecule pages sorted by species (human/mouse)
•  Directly access PubMed records for each annotation
•  Share your analysis results with other IPA registered users
•  Can also share only part of the result
•  Import external pathways into IPA (in SBML format)
•  Use Path Designer to edit pathway/network diagrams
•  MicroRNA target filter
•  Biomarker analysis
•  Export data and images for reports/publications
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Upload the data
•  Data in a structured format (excel, tab-delimited, etc.)
•  Limit the header to only the first row
•  Keep the ‘flexible format’ option (default)
•  Identifier type: Automatic, but change if inappropriate
•  Select only the columns that you want to upload and ignore the rest
•  Select appropriate units like fold change, z-score, p-value, etc.
•  Prompts you to create a new project; all your analysis results will be
stored in this project folder, which can be accessed from the left panel
•  General default setting are good unless you want to customize
•  Step-wise directions are available at
•  http://ingenuity.force.com/ipa/IPATutorials?id=kA150000000TPy1#
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Running Core Analysis
•  Mapped Ids: Identified by the IPA database
•  Unmapped Ids: Unidentified by the IPA database
•  Analysis –ready molecules: Identified and also contain
information in the database
•  Run the analysis for individual observations
•  If more than one observation is selected, analysis is run
independently for each and saved under separate names
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Network/Pathway Analysis
•  Grow: Connected molecules for a selected molecule can be grown
based on the known connections in the literature
•  Trim: Connections can be removed from a larger network based on
certain criteria
•  Connect: Two sets of unconnected genes can be connected via the
shortest path
•  Pathway Explorer: Above tools can be used to explore pathways
•  Pathway Designer: Offers graphical representation of molecules for
generating publication quality figures
•  Canonical pathways can be selected and genes from the dataset can
be overlaid
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