Difference between revisions of "BIN-PPI-Analysis"

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<b>Deliverables:</b><br />
 
<b>Deliverables:</b><br />
 
<section begin=deliverables />
 
<section begin=deliverables />
−
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-time_management" -->
+
<li><b>Time management</b>: 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.</li>
−
*<b>Time management</b>: 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.
+
<li><b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.</li>
−
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-journal" -->
+
<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
−
*<b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.
 
−
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-insights" -->
 
−
*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
 
 
<section end=deliverables />
 
<section end=deliverables />
 
<!-- ============================  -->
 
<!-- ============================  -->
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<section begin=prerequisites />
 
<section begin=prerequisites />
 
<b>Prerequisites:</b><br />
 
<b>Prerequisites:</b><br />
−
<!-- included from "./data/ABC-unit_components.txt", section: "notes-external_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:<br />
−
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:
 
−
<!-- included from "./data/ABC-unit_prerequisites.txt", section: "bch" -->
 
−
<!-- included from "./data/ABC-unit_prerequisites.txt", section: "biomolecules" -->
 
 
*<b>Biomolecules</b>: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function.
 
*<b>Biomolecules</b>: The molecules of life; nucleic acids and amino acids; the genetic code; protein folding; post-translational modifications and protein biochemistry; membrane proteins; biological function.
−
<!-- included from "./data/ABC-unit_prerequisites.txt", section: "metabolism" -->
 
 
*<b>Metabolism</b>: Enzymatic catalysis and control; reaction sequences and pathways; chemiosmotic coupling; catabolic- and anabolic pathways.
 
*<b>Metabolism</b>: Enzymatic catalysis and control; reaction sequences and pathways; chemiosmotic coupling; catabolic- and anabolic pathways.
−
<!-- included from "./data/ABC-unit_prerequisites.txt", section: "cellular_components" -->
 
 
*<b>Organelles</b>: Compartmentalization, organelles and structures of the cell; the extracellular matrix.
 
*<b>Organelles</b>: Compartmentalization, organelles and structures of the cell; the extracellular matrix.
−
<!-- included from "./data/ABC-unit_components.txt", section: "notes-prerequisites" -->
+
This unit builds on material covered in the following prerequisite units:<br />
−
This unit builds on material covered in the following prerequisite units:
 
 
*[[BIN-PPI-Databases|BIN-PPI-Databases (Protein-Protein Interaction Databases)]]
 
*[[BIN-PPI-Databases|BIN-PPI-Databases (Protein-Protein Interaction Databases)]]
 
*[[FND-PPI-Physical_vs_genetic|FND-PPI-Physical_vs_genetic (Physical- vs. Genetic Interactions)]]
 
*[[FND-PPI-Physical_vs_genetic|FND-PPI-Physical_vs_genetic (Physical- vs. Genetic Interactions)]]
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=== Evaluation ===
 
=== Evaluation ===
−
<!-- included from "./components/BIN-PPI-Analysis.components.txt", section: "evaluation" -->
 
  
−
This learning unit can be evaluated for a maximum of 6 marks. If you want to submit tasks for this unit for credit you have the following options. If you have any questions about these options, discuss on the mailing list.
+
This learning unit can be evaluated for a maximum of 5 marks. There are several options for submission. Choose one option, then ...
 +
<ol>
 +
<li>Create a new page on the student Wiki as a subpage of your User Page.</li>
 +
<li>Put all of your writing to submit on this one page.</li>
 +
<li>When you are done with everything, go to the [https://q.utoronto.ca/courses/180416/assignments 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'''.</li>
 +
</ol>
 +
 
 +
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.
 +
 
 +
{{Smallvspace}}
  
 
;Task submission option
 
;Task submission option
 
:# Create a new page on the student Wiki as a subpage of your User Page.
 
:# Create a new page on the student Wiki as a subpage of your User Page.
 
:# The R code for this unit contains at its end a short task. Put your submission for this task on your page.
 
:# The R code for this unit contains at its end a short task. Put your submission for this task on your page.
−
:# When you are done with everything, add the following category tag to the page:
+
:# Follow the instructions very carefully, especially regarding the "seal" of the list of genes.
−
::<code><nowiki>[[Category:EVAL-BIN-PPI-Analysis]]</nowiki></code>
+
:# Note: this task requires '''interpretation''' of your results. Merely listing the genes is not enough. What do these genes have in common (or not)?
−
:'''Do not''' change your submission page after this tag has been added. The page will be marked and the category tag will be removed by the instructor.
+
:# When you are done, submit the link to your page via Quercus as described above.
  
 +
<!--
 
; Quiz option
 
; Quiz option
 
: Open the [http://steipe.biochemistry.utoronto.ca/abc/students/index.php/Signup-BIN-PPI-Analysis_Quiz  '''signup-page for the quiz for this unit (linked from here)'''] and add your name. Your name must be signed up by 12:00 of the day of the Quiz to ensure copies of the quiz are available for all participants.
 
: Open the [http://steipe.biochemistry.utoronto.ca/abc/students/index.php/Signup-BIN-PPI-Analysis_Quiz  '''signup-page for the quiz for this unit (linked from here)'''] and add your name. Your name must be signed up by 12:00 of the day of the Quiz to ensure copies of the quiz are available for all participants.
−
<!-- included from "./data/ABC-unit_components.txt", section: "quiz-mechanics" -->
+
<div style="margin-left: 2rem;">Quizzes will be written in class, back-to-back if there is more than one quiz scheduled. We may begin at any time. We will have an open-ended Q&A session before the quiz. You can't take the quiz if you are not present in class when the question sheets are handed out, so don't be late. Once all scheduled quizzes are written, we will discuss and mark them. You will mark your own quiz. All marking must be done with a red pen - so you '''must''' bring a red pen to class in order to participate. The mark you give yourself may be revised by the instructor after spot-checking quizzes. If this is necessary, you will be notified. You must mark your quiz correctly and honestly - don't get into trouble with academic integrity rules: it will be an academic offence if you mark questions as correct that were discussed in class and should have been marked incorrect. When in doubt, ask.</div>
−
:Quizzes will be written in class, back-to-back if there is more than one quiz scheduled. We may begin at any time. We will have an open-ended Q&A session before the quiz. You can't take the quiz if you are not present in class when the question sheets are handed out, so don't be late. Once all scheduled quizzes are written, we will discuss and mark them. You will mark your own quiz. All marking must be done with a red pen - so you '''must''' bring a red pen to class in order to participate. The mark you give yourself may be revised by the instructor after spot-checking quizzes. If this is necessary, you will be notified. You must mark your quiz correctly and honestly - don't get into trouble with academic integrity rules: it will be an academic offence if you mark questions as correct that were discussed in class and should have been marked incorrect. When in doubt, ask.
+
-->
  
 
<!--
 
<!--
 
; R-code option
 
; R-code option
 
:Submit code according to the following requirements. Make sure your code is documented.
 
:Submit code according to the following requirements. Make sure your code is documented.
 +
-->
  
−
 
+
;Option to write a "Self-Evaluation Question"
−
; Option to write a "Self-Evaluation Question"
+
: You can submit a "Self-Evaluation Question" for at most '''one''' of your  assignments.
−
:If you submit both [[BIN-NCBI]] and [[BIN-EBI]] for evaluation, you can choose this option for only one of the two.
+
: 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 [[ABC-Rubrics| '''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|'''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.
−
: 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 [[ABC-Rubrics| '''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|'''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.
+
:# Create a new page on the student Wiki as a subpage of your User Page. Develop your question there.
−
:#Create a new page on the student Wiki as a subpage of your User Page. Develop your question there.
+
:# When you are done, submit the link to your page via Quercus as described above
−
:#When you are done with developing this contents, add the following category tag to the page:
 
−
::<code><nowiki>[[Category:EVAL-BIN-NCBI]]</nowiki></code>
 
−
:'''Do not''' change your submission page after this tag has been added. The page will be marked and the category tag will be removed by the instructor.
 
−
-->
 
  
 
== Contents ==
 
== Contents ==
−
<!-- included from "./components/BIN-PPI-Analysis.components.txt", section: "contents" -->
 
  
 
{{Task|1=
 
{{Task|1=
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=== Optional: Cytoscape ===
 
=== Optional: Cytoscape ===
  
−
{{Vspace}}
+
{{Smallvspace}}
  
−
;This is all that is required. There is optional material below that you may find interesting.
+
;This is all that is required. There is optional material below that you may find useful.
  
−
{{Vspace}}
+
{{Smallvspace}}
  
 
If you work a lot with interaction networks, sooner or later you will come across [http://www.cytoscape.org/ Cytoscape]. It is more or less the standard among "professional" systems biologists. But it is not an online tool.
 
If you work a lot with interaction networks, sooner or later you will come across [http://www.cytoscape.org/ 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 [http://www.systemsbiology.org/ 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.
 
Cytoscape was originally written in Trey Ideker's lab at the [http://www.systemsbiology.org/ 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.
−
 
−
{{#pmid:21063955}}
 
  
 
{{task|1=
 
{{task|1=
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== Self-evaluation ==
 
−
<!--
 
−
=== Question 1===
 
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Question ...
 
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<div class="toccolours mw-collapsible mw-collapsed" style="width:800px">
 
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Answer ...
 
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<div class="mw-collapsible-content">
 
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Answer ...
 
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</div>
 
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  </div>
 
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  {{Vspace}}
 
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== Notes ==
 
−
<!-- included from "./components/BIN-PPI-Analysis.components.txt", section: "notes" -->
 
−
<!-- included from "./data/ABC-unit_components.txt", section: "notes" -->
 
−
<references />
 
−
== Further reading, links and resources ==
 
−
{{#pmid: 15608232}}
 
−
<!-- {{WWW|WWW_GMOD}} -->
 
−
<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
 
  
 
{{Vspace}}
 
{{Vspace}}
  
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<!-- included from "./data/ABC-unit_components.txt", section: "ABC-unit_ask" -->
 
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----
 
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{{Vspace}}
 
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−
<b>If in doubt, ask!</b> If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.
 
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−
----
 
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{{Vspace}}
 
  
 
<div class="about">
 
<div class="about">
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:2017-08-05
 
:2017-08-05
 
<b>Modified:</b><br />
 
<b>Modified:</b><br />
−
:2017-11-09
+
:2020-10-07
 
<b>Version:</b><br />
 
<b>Version:</b><br />
−
:1.0
+
:1.2
 
<b>Version history:</b><br />
 
<b>Version history:</b><br />
 +
*1.2 Edit policy update
 +
*1.1 2020 Updates; revised assignments. Now using STRING v. 11
 
*1.0 First live version
 
*1.0 First live version
 
*0.1 First stub
 
*0.1 First stub
 
</div>
 
</div>
−
[[Category:ABC-units]]
 
−
<!-- included from "./data/ABC-unit_components.txt", section: "ABC-unit_footer" -->
 
  
 
{{CC-BY}}
 
{{CC-BY}}
  
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[[Category:ABC-units]]
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{{UNIT}}
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{{LIVE}}
 
</div>
 
</div>
 
<!-- [END] -->
 
<!-- [END] -->

Latest revision as of 05:01, 10 October 2020

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.

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.

    • 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:


     



     



     


    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:


     

    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

    CreativeCommonsBy.png This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.

    Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=BIN-PPI-Analysis&oldid=11842"