Bioinformatics Training and Education Program

Pathway Analysis Workshop (2-day)

Pathway Analysis Workshop (2-day)

 When: Dec. 17th, 2014 - Dec. 18th, 2014 9:30 pm - 4:30 pm

To Know

Class Files:
This class has ended.

About this Class

Day 1 - AM (9:30 AM – 12:30 PM)  Ingenuity IPA -  Basic Training 
(Kate Wendelsdorf, Ph.D. - Ingenuity Pathway Analysis)
Ingenuity IPA® is the industry leading software solution to model, analyze, and understand complex biological and chemical systems foundational to human health and disease. Quickly identify biological relationships, mechanisms, pathways, functions and diseases most relevant to experimental datasets. IPA is cited in >10,000 peer-reviewed articles.
Getting Started

  • Fundamentals of IPA
  • Overview of key features
  • Search & Pathway Building
  • Advanced Search
  • Building & editing pathways
  • Using Build & Overlay tools

Day 1 - PM - (1:30 PM – 4:30 PM)  Ingenuity IPA -  Data Analysis
(Kate Wendelsdorf, Ph.D. - Ingenuity Pathway Analysis)
Dataset Analysis 

  • Data Upload & Analysis
  • Interpretation of Gene, Transcript, Protein & Metabolite Data
  • Pathway Analysis & Canonical Pathways
  • Downstream Effects &vInterpreting the Heat Map
  • Upstream Regulators & Regulator Effects Analysis
  • Interpreting networks
  • Comparison & multiple observations analysis

Day 2 - AM (9:30 AM – 12:30 PM) MetaCore - Introductory Topics
(Matthew Wampole, Ph.D. - Thomson Reuters Metacore)
MetaCore™ is an integrated curated knowledge database and software suite for pathway analysis of experimental data and gene lists. The scope of data types includes microarray and sequence-based gene expression, SNPs and CGH arrays, RNAi screens, gene variants, proteomics, metabolomics, Co-IP pull-out and other custom interactions which can all by analyzed in tandem. MetaCore™ is based on a proprietary manually-curated database of human protein-protein, protein-DNA and protein-compound interactions, metabolic and signaling pathways for human, mouse and rat, supported by proprietary ontologies and controlled vocabulary. The analytical package includes easy-to-use, intuitive tools for searching and data visualization, enabling the identification of the most relevant biological pathways, networks, and processes in our “virtual lab.”

  • General Overview: Thomson Reuters Systems Biology Solutions    
  • Knowledge Mining: Explore the database and exporting
  • Uploading, filtering and setting a background·  
  • Running Functional Enrichments and exploring Pathway Maps
  • Running Workflows

Day 2 - AM (1:30 AM – 4:30 PM) MetaCore - Advanced Topics
(Matthew Wampole, Ph.D. - Thomson Reuters Metacore)

  • Interactome Analysis: Finding key hubs in your data
  • Microarray Repository: Using and comparing public datasets
  • Network Building: When to use each algorithm


  • Example20Prostate20Data.xls: |
  • IPA_getting_started_CA_SE.docx: |
  • IPA_getting_started_CA_SE_0.docx: |
  • Example20Data.txt: |