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 |
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 |
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