BIN-PPI-Analysis

PPI Analysis

(Analysis of PPIs; Totality, context; date- and party hubs; dynamics; Cytoscape)

 

Abstract:

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

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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.

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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.

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Prerequisites:
You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources:

• Biomolecules: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function.
• Metabolism: Enzymatic catalysis and control; reaction sequences and pathways; chemiosmotic coupling; catabolic- and anabolic pathways.
• Organelles: Compartmentalization, organelles and structures of the cell; the extracellular matrix.

This unit builds on material covered in the following prerequisite units:

• BIN-PPI-Databases (Protein-Protein Interaction Databases)
• FND-PPI-Physical_vs_genetic (Physical- vs. Genetic Interactions)

 

 

 

Evaluation

This learning unit can be evaluated for a maximum of 5 marks. There are several options for submission. Choose one option, then ...

1. Create a new page on the student Wiki as a subpage of your User Page.
2. Put all of your writing to submit on this one page.
3. When you are done with everything, go to the Quercus Assignments page and open the first Learning Unit that you have not submitted yet. Paste the URL of your Wiki page into the form, and click on Submit Assignment.

Your link can be submitted only once and not edited. But you may change your Wiki page at any time. However only the last version before the due date will be marked. All later edits will be silently ignored.

 

Task submission option

1. Create a new page on the student Wiki as a subpage of your User Page.
2. The R code for this unit contains at its end a short task. Put your submission for this task on your page.
3. Follow the instructions very carefully, especially regarding the "seal" of the list of genes.
4. Note: this task requires interpretation of your results. Merely listing the genes is not enough. What do these genes have in common (or not)?
5. When you are done, submit the link to your page via Quercus as described above.

Option to write a "Self-Evaluation Question"

You can submit a "Self-Evaluation Question" for at most one of your assignments.

Write a "Self-evaluation Question" (with a model solution) that explores a significant, non-trivial aspect of studying how to work with EBI resources within this learning unit. Ensure that the question is feasible, given the existing content of the unit - or coordinate an extension of the contents with your instructor. Ensure your question pursues a high-level learning goal, it should allow others to demonstrate understanding, critical analysis, and/or the capacity to integrate and synthesize knowledge, not merely test memorization. Ensure that your question is specific, not ambiguous, vague or tangential to the contents. Ensure you are testing valuable knowledge and skills, not Cargo Cult. Apply the marking rubrics in spirit, to satisfy yourself of the quality of your contribution. Obviously, details of evaluation will vary with the question. Use the format and code templates that you find on the Self evaluation questions page - but don't assume those examples are already models of excellent contributions. Note: assume that approximately the same amount of work is expected for all evaluation options. Consequently, the standard of excellence for this option will be quite high.

1. Create a new page on the student Wiki as a subpage of your User Page. Develop your question there.
2. When you are done, submit the link to your page via Quercus as described above

Contents

Task:

• Read the introductory notes on the analysis of Protein-Protein Interaction (PPI) networks.

 

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.
• 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.

 

About ...
 
Author:

Boris Steipe <boris.steipe@utoronto.ca>

Created:

2017-08-05

Modified:

2020-10-07

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

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