Welcome to Pathways and Network Analysis of -Omics Data 2020.

Class Materials

You can download the printed course manual here.

Workshop Schedule

Pre-Workshop Materials and Laptop Setup Instructions

Laptop Setup Instructions

A Check list to setup your laptop can be found here

Install these tools on your laptop before coming to the workshop:

Basic programs

  1. A robust text editor:
  2. A file decompression tool.
    • For Windows/PC – 7zip.
    • For Linux – gzip.
    • For Mac – already there.
  3. A robust internet browser such as:
    • Firefox
    • Safari
    • Chrome
  4. A PDF Viewer
    • Adobe Acrobat or equivalent

Java 11 Installation

We will be using Cytoscape and GSEA both of which require Java 11. Before proceeding, check to see if you already have Java 11 installed:

If you do not have Java installed or you have an older version of Java installed please proceed with the following steps:

  1. Download and install Java 11:
    • Go to https://www.oracle.com/java/technologies/javase-jdk11-downloads.html
    • create a free Oracle account - Top right hand corner --> View Accounts --> Create Account
    • Download the java installer that corresponds to your platform (MAC, Windows or Linux)
    • Open the installer and follow the steps
    • An "Install Succeeded" should appear at the end of the installer dialog box
    • You can check that you correctly installed java by typing java -version in terminal window

Cytoscape Installation

Please install the latest version of Cytoscape 3.8.0 as well as a group of Cytoscape Apps that we will be using for different parts of the course.

  1. Install Cytoscape 3.8.0:
    • Go to: https://cytoscape.org/download-platforms.html
    • Choose the version corresponding to your operating system (OS, Windows or UNIX)
    • Follow instructions to install cytoscape
    • Verify that Cytoscape has been installed correctly by launching the newly installed application
    • Contact your system administrator if you have trouble with Java installation
  2. WInstall the following Cytoscape Apps - Apps are installed from within Cytoscape. In order to install Apps launch Cytoscape
    • From the menu bar, select ‘Apps’, then ‘App Manager’.
    • Within 'all apps', search for the following and install:
    • EnrichmentMap 3.3.0
    • EnrichmentMap Pipeline Collection 1.0.0 (it will install ClusterMaker2, WordCloud and AutoAnnotate)
    • GeneMANIA 3.5.2
    • IRegulon 1.3
    • ReactomeFIPlugin 7.2.3 - http://apps.cytoscape.org/apps/reactomefiplugin
    • stringApp 1.5.1
    • yFiles Layout Algorithms 1.1
  3. Install the data set within GeneMANIA app. This requires time and a good network connection to download completely (~15mins)
    • From the menu bar, select ‘Apps’, hover over ‘GeneMANIA’, then select ‘Choose Another Data Set’.
    • From the list of available data sets, select the most recent and under ‘Include only these networks:’ select ‘all’. Click on ‘Download’.
    • An ‘Install Data’ window will pop-up. Select H.Sapiens Human (2589 MB). Click on ‘Install’.

GSEA Installation

Please install the latest version of GSEA (4.0.3)

  1. Download GSEA
    • Go to the GSEA page
    • Register (using an institutional email address)
    • Login
    • Locate the Download page and download the version corresponding to your system
    • MAC users: download GSEA_4.0.3.app.zip
    • Window users: download GSEA_Win_4.0.3-installer.exe
    • Unix users: download GSEA_Linux_4.0.3.zip
    • Launch GSEA to test it.
  2. Download GSEA for command line : this is necessary for all platform users to run GSEA from a script (integrated workflow on day 3)
    • Download GSEA_4.0.3.zip (and keep it for later use during the workshop)

Pre-workshop Tutorials

It is in your best interest to complete these before the workshop.

Pre-workshop Readings and Lectures

  1. Video Module 1 - Introduction to Pathway and Network Analysis by Gary Bader
  2. Video Module 5 - Gene Function Prediction (GeneMania) by Quaid Morris
  3. Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap Reimand J, Isserlin R, Voisin V, Kucera M, Tannus-Lopes C, Rostamianfar A, Wadi L, Meyer M, Wong J, Xu C, Merico D, Bader GD Nat Protoc. 2019 Feb;14(2):482-517 - Available here as well

Additional tutorials

Interacting with Cytoscape using CyRest and command lines (for advanced users): https://github.com/cytoscape/cytoscape-automation/blob/master/for-scripters/R/advanced-cancer-networks-and-data-rcy3.Rmd