Expected Preparations:

  Biomolecules:
The molecules of life; The genetic code; Nucleic acids; Amino acids; Protein folding; Post-translational modifications and protein biochemistry; Membrane proteins; Biological function.
   [BIN-PPI]
Databases 		  [FND-PPI]
Physical_vs_genetic 		 
  If you are not already familiar with the prior knowledge listed above, you need to prepare yourself from other information sources.   The units listed above are part of this course and contain important preparatory material.  
Keywords: Analysis of PPIs; Totality; context; date- and party hubs; dynamics; Cytoscape
Objectives:

This unit will …

  • … introduce concepts of PPI network analysis;

  • … demonstrate this in practice with a sample human interaction network.

 Outcomes:

After working through this unit you …

  • … can load and analyze a network from STRING data;

  • … can annotate selected nodes using BioMART.

Deliverables:

Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.

Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don’t overlook these.

Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.

Evaluation:

Evaluation deliverables under revision:
While we are rebalancing formative feedback (advice) and summative feedback (grades) for this course, please ignore all instructions for the submission of assignments until this alert is removed.

 

Contents

This unit contains a brief introduction to the analysis of biological networks.

Task…

 

Task…

  • Open RStudio and load the ABC-units R project. If you have loaded it before, choose File ▸ Recent projects ▸ ABC-Units. If you have not loaded it before, follow the instructions in the RPR-Introduction unit.
  • Choose Tools ▸ Version Control ▸ Pull Branches to fetch the most recent version of the project from its GitHub repository with all changes and bug fixes included. This ensures that your data and code remain up to date when we update, or fix bugs.
  • Type init() if requested.
  • Open the file BIN-PPI-Analysis.R and follow the instructions.

     

    Note: take care that you understand all of the code in the script. Evaluation in this course is cumulative and you may be asked to explain any part of code.

 

Optional: Cytoscape

 

This is all that is required. There is optional material below that you may find useful.

 

If you work a lot with interaction networks, sooner or later you will come across Cytoscape. It is more or less the standard among “professional” systems biologists. But it is not an online tool. Cytoscape was originally written in Trey Ideker’s lab at the Institue for Systems Biology; it is now a thriving, open-source community project for the development of a biology-oriented network display and analysis tools.

Task…

  • Navigate to the Cytoscape homepage and inform yourself what the program does and how to install it. There are many tutorials online available. But this is software that needs to be downloaded, and installed and it definitively has a learning curve.

Questions, comments

If in doubt, ask! If anything about this contents is not clear to you, do not proceed but ask for clarification. If you have ideas about how to make this material better, let’s hear them. We are aiming to compile a list of FAQs for all learning units, and your contributions will count towards your participation marks.

Improve this page! If you have questions or comments, please post them on the Quercus Discussion board with a subject line that includes the name of the unit.

References

Page ID: BIN-PPI-Analysis

Author:
Boris Steipe ( <boris.steipe@utoronto.ca> )
Created:
2017-08-05
Last modified:
2022-09-14
Version:
1.2
Version History:
–  1.2 Edit policy update
–  1.1 2020 Updates; revised assignments. Now using STRING v. 11
–  1.0 First live version
–  0.1 First stub
Tagged with:
–  Unit
–  Live
–  Evaluated unit
–  Has lecture slides
–  Links to R course project

 

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