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Introduction

Various types of molecular interactions are principal determinants of the system-scale behaviour of the cell. These interactions include protein–protein interaction, metabolic, signaling and transcription-regulatory networks. Recent innovations and continuing falling costs of technologies have enabled researchers to catalogue the component molecules of these networks not only at a genome-wide scale but also under a large number of different experimental conditions (e.g. time points, cell types, stimuli and treatments). In this tutorial, we will use Discovery Environment apps to analyze a sample dataset of five transcription factors that control the rate of ~14k genes.

Some experience with python programming and command-line is required to follow this tutorial. Download code and sample data for this tutorial from the github repo.

Learning Objectives

  • Intro to network analysis and visualization
  • Why networks are difficult to visualize and understand
  • Powerful combination of tools and techniques to do network analysis
  • How to manipulate, slice, and dice networks in order to analyze large networks
  • Using CyVerse Discovery Environment apps to do network analysis and visualization

Tutorial Maintainer(s)

Who to contact if this guide needs fixing. You can also email learning@CyVerse.org

Maintainer Institution Contact
Iqbal Hossain CyVerse / UA hossain@arizona.edu
Reetu Tuteja CyVerse / UA reetututeja@cyverse.org 
.. toctree::
        :maxdepth: 2

        Step One <step1.rst>
  Perform network analysis using Discovery Environment VICE app <step2.rst>
  Further Reading <step3.rst>

Prerequisites

Downloads, access, and services

In order to complete this tutorial you will need access to the following services/software

Prerequisite Preparation/Notes Link/Download
CyVerse account You will need a CyVerse account to complete this exercise |CyVerse User Portal|
Cyberduck Standalone software for upload/download to Data Store Download Cyberduck

Platform(s)

We will use the following CyVerse platform(s):

Platform Interface Link Platform Tour
Data Store GUI/Command line |Data Store| |Data Store Guide|
Discovery Environment Web/Point-and-click |Discovery Environment| |Discovery Environment Guide|

Application(s) used

Discovery Environment App(s):

App name Version Description App link Notes/other links
Jupyterlab-GraphViz 1.0 JupyterLab with Graphviz package CyVerse launch Original App Documentation

Input and example data

In order to complete this tutorial you will need to have the following inputs prepared

Input File(s) Format Preparation/Notes Example Data
query.cyjs Cytoscape json Data downloaded from ConnecTF iplantcollaborative > example_data > Network_analysis_webinar

Fix or improve this documentation

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