Course Details

  • Date: June 2nd, 2015 - June 2nd, 2015
  • Time: 9:30 am - 4:30 pm
  • Location: Bldg 10: FAES Classroom 3 (B1C207)
  • Presenter(s): Parthav Jailwala (CCBR)

This workshop will cover some basic concepts involved in the integration of different types of NGS data in order to obtain a better overall picture of the underlying biology. Specifically, the course will examine the integration of micro RNA and mRNA expression data as well as methylation, mutation and copy number alteration as they relate to mRNA expression.  Topics covered in the lecture components will be complemented by hands-on sessions with software from Partek, cBioPortal and Qlucore.

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.

AM 9:30-11:00 – Introductory Lecture

(Anand Merchant MD, PhD – CCBR)

  • Concepts 
  • Data types
  • Modalities
  • Challenges
  • Example Workflows
  • Hands-on exercise (Partek/IPA)

    • Genomics Data Integration (mRNA/miRNA)


AM 11:00-12:00 – NGS Data Integration (cBioPortal)

(Parthav Jailwala, MSc- CCBR)

The cBioPortal for Cancer Genomics ( provides a Web resource for exploring, visualizing and analyzing multidimensional cancer genomics data that is curated from large scale cancer genomic data sets. Users can visualize patterns of gene alterations across samples in a cancer study, compare gene alteration frequencies across multiple cancer studies, or summarize all relevant genomic alterations in an individual tumor sample. Genomic data types integrated by cBioPortal include somatic mutations, DNA copy-number alterations (CNAs), mRNA and microRNA (miRNA) expression and DNA methylation. 
In this session, followed by an introductory overview of data integration in cBioPortal, we will carry out a brief hands-on exercise of querying and visualizing different data-types in TCGA related to a few key genes in human GBM.
  • Introductory Lecture
  • Hands on with FireBrowse and cBioPortal
PM 1:30-4:30 Qlucore Omics Explorer – Basic Training & Data Integration

(Carl Johan Ivarsson)

  • Introduction and Live demonstration ~ 30 min

    • Introduction and terminology
    • Visualize data using PCA
    • Identify discriminating variables using basic statistical tests
    • Export variable lists and images
    • Presentation of data in different plot types
    • Integrate data sets
  • Basic Hands-on Training including Data Integration methylation/mRNA ~ 2 hours

    • Visualize (PCA, color according to annotation)
    • Identify discriminating variables (t-test)
    • Create Variable Lists
    • Present the results in different plots (heat map and box plot)
    • Data Integration – mRNA/methylation

 Direction of FAES Classrooms (B1C207) can be found here