iPathwayGuide Workshop
When: Dec. 19th, 2016 9:30 am - 4:00 pm
To Know
Where:
NIH Bldg 10, FAES Room 4 (B1C205)
Organizer:
BTEP
Presented By:
Cordelia Ziraldo (Advaita Bioinformatics)
Class Files:
About this Class
iPathwayGuide is a gene and protein expression analysis tool that uses a systems biology approach to identify significantly impacted pathways, gene ontology terms, diseases, and predicted microRNAs based on the given gene or protein differential expression signature. It uses an advanced pathway analysis approach that considers the role, positioning, and relationships of a given gene within a pathway, resulting in a significantly fewer false positives associated with pathway analysis.
More information can be found at this link: http://www.advaitabio.com/ipathwayguide.html
PLEASE NOTE: This 1-day workshop is a BYOC (Bring your own Laptop Computer) class. Government issued or personal computers are permitted. We will be able to supply a very limited set of computers, so if you want to take the class but cannot bring your own computer please indicate such in the Comment section on the registration form.
The software is designed to work with all the latest major browser platforms: Google Chrome, Mozilla Firefox, Apple Safari (Mac only, iOS not supported yet), as well as Microsoft Internet Explorer 11 (though some image download capabilities may not function).
WORKSHOP AGENDA - Monday, Dec 19, 2016
Morning Session
9:30 am -10:55 am
Introduction to iPathwayGuide
- Overview: modules, User Interface (UI), cloud access, sharing
- Scoring Method: Impact Analysis, types of evidence, multiple correction
- Advanced features: printable report & meta-analysis
Uploading data: lecture & follow along w/ demo
- Data Analysis Pipeline
- Supported organisms and file types
- Uploading CEL files
- Custom format: gene symbol, log-fold change, p-values
- Thresholds for DE
- TRY: Upload GEO2R file
- TRY: Fill in Title & Description, Contrast Names
- TRY: Choose thresholds for Differential Expression
11:05 am -12:30 pm Follow along w/ demo
Dataset 1: NanoString Pan-Cancer panel, Breast Cancer samples (human primary tissue)
- Impact Analysis
- Dataset background
- TRY: Accept share
- Summary Page
- DE Genes
- Pathways
- Printable report
- Q&A
12:30 - 1:00 pm LUNCH BREAK
Afternoon session
1:00 pm - 2:25 pm Hands-on practice
Dataset 2: Genome-wide analysis of gene expression regulated by VRK1 kinase in cancer cell lines (GSE86942)
- miRNA Inference
- Gene Ontologies
- Diseases
- TRY: Share Report
- TRY: Generate Meta-analysis, Identify biomarkers, Export Results
- Q&A
2:35 pm - 4:00 pm Data Analysis Exercise
Dataset 3: Anaplastic Large Cell Lymphoma of Childhood (GSE78513, human primary tissue)
- TRY: Accept share
- Send a request for help/ feedback
- Generate meta-analysis
- Select comparable contrasts
- Identify putative mechanisms on a high impact pathway
- Identify probable miRNAs
- Identify relevant GO Terms
- Identify relevant diseases
- Generate printable report
- Design a meta-analysis study
- Which combination of regions is appropriate?
- Which modules are informative?
- Results: view rank diagram, find biomarkers
- Export pertinent figures & tables
- Share via email
- Report findings to class
- Q&A