Difference between revisions of "BIN-PPI-Analysis"

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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce; font-size:300%; font-weight:400; color: #000000; width:100%;">
 
PPI Analysis
 
PPI Analysis
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  </div>
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<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#b3dbce; font-size:30%; font-weight:200; color: #000000; ">
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(Analysis of PPIs; Totality, context; date- and party hubs; dynamics; Cytoscape)
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  {{Vspace}}
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</div>
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<div class="keywords">
 
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<b>Keywords:</b>&nbsp;
 
−
Analysis of PPIs; Totality, context; date- and party hubs; dynamics; Cytoscape
 
 
</div>
 
</div>
  
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{{Vspace}}
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{{Smallvspace}}
  
  
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__TOC__
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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce33; font-size:85%;">
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<div style="font-size:118%;">
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{{Vspace}}
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<b>Abstract:</b><br />
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{{DEV}}
 
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</div>
 
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<div id="ABC-unit-framework">
 
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== Abstract ==
 
 
<section begin=abstract />
 
<section begin=abstract />
−
<!-- included from "../components/BIN-PPI-Analysis.components.wtxt", section: "abstract" -->
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This unit contains a brief introduction to the analysis of biological networks.
−
...
 
 
<section end=abstract />
 
<section end=abstract />
−
 
+
</div>
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{{Vspace}}
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<!-- ============================  -->
−
 
+
<hr>
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<table>
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== This unit ... ==
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<tr>
−
=== Prerequisites ===
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<td style="padding:10px;">
−
<!-- included from "../components/BIN-PPI-Analysis.components.wtxt", section: "prerequisites" -->
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<b>Objectives:</b><br />
−
<!-- included from "ABC-unit_components.wtxt", section: "notes-external_prerequisites" -->
+
This unit will ...
−
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:
+
* ... introduce concepts of PPI network analysis;
−
<!-- included from "FND-prerequisites.wtxt", section: "bch" -->
+
* ... demonstrate this in practice with a sample human interaction network.
−
<!-- included from "FND-prerequisites.wtxt", section: "biomolecules" -->
+
</td>
 +
<td style="padding:10px;">
 +
<b>Outcomes:</b><br />
 +
After working through this unit you ...
 +
* ... can load and analyze a network from STRING data;
 +
* ... can annotate selected nodes using BioMART.
 +
</td>
 +
</tr>
 +
</table>
 +
<!-- ============================ -->
 +
<hr>
 +
<b>Deliverables:</b><br />
 +
<section begin=deliverables />
 +
<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>
 +
<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>
 +
<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
 +
<section end=deliverables />
 +
<!-- ============================  -->
 +
<hr>
 +
<section begin=prerequisites />
 +
<b>Prerequisites:</b><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:<br />
 
*<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 "FND-prerequisites.wtxt", 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 "FND-prerequisites.wtxt", 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 "ABC-unit_components.wtxt", section: "notes-prerequisites" -->
+
This unit builds on material covered in the following prerequisite units:<br />
−
You need to complete the following units before beginning this one:
+
*[[BIN-PPI-Databases|BIN-PPI-Databases (Protein-Protein Interaction Databases)]]
−
*[[FND-PPI-Physical_vs_genetic]]
+
*[[FND-PPI-Physical_vs_genetic|FND-PPI-Physical_vs_genetic (Physical- vs. Genetic Interactions)]]
 +
<section end=prerequisites />
 +
<!-- ============================  -->
 +
</div>
  
−
{{Vspace}}
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{{Smallvspace}}
  
  
−
=== Objectives ===
 
−
<!-- included from "../components/BIN-PPI-Analysis.components.wtxt", section: "objectives" -->
 
−
...
 
  
−
{{Vspace}}
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{{Smallvspace}}
  
  
−
=== Outcomes ===
+
__TOC__
−
<!-- included from "../components/BIN-PPI-Analysis.components.wtxt", section: "outcomes" -->
 
−
...
 
  
 
{{Vspace}}
 
{{Vspace}}
  
  
−
=== Deliverables ===
+
=== Evaluation ===
−
<!-- included from "../components/BIN-PPI-Analysis.components.wtxt", section: "deliverables" -->
+
 
−
<!-- included from "ABC-unit_components.wtxt", section: "deliverables-time_management" -->
+
This learning unit can be evaluated for a maximum of 5 marks. There are several options for submission. Choose one option, then ...
−
*<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.
+
<ol>
−
<!-- included from "ABC-unit_components.wtxt", section: "deliverables-journal" -->
+
<li>Create a new page on the student Wiki as a subpage of your User 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.
+
<li>Put all of your writing to submit on this one page.</li>
−
<!-- included from "ABC-unit_components.wtxt", section: "deliverables-insights" -->
+
<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>
−
*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
+
</ol>
  
−
{{Vspace}}
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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
 +
:# 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.
 +
:# Follow the instructions very carefully, especially regarding the "seal" of the list of genes.
 +
:# Note: this task requires '''interpretation''' of your results. Merely listing the genes is not enough. What do these genes have in common (or not)?
 +
:# When you are done, submit the link to your page via Quercus as described above.
  
−
=== Evaluation ===
+
<!--
−
<!-- included from "../components/BIN-PPI-Analysis.components.wtxt", section: "evaluation" -->
+
; Quiz option
−
<!-- included from "ABC-unit_components.wtxt", section: "eval-INT-TBD" -->
+
: 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.
−
<b>Evaluation: Integrated Unit</b><br />
+
<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>
−
:This unit should be submitted for evaluation for a maximum of 10 marks. Details TBD.
+
-->
  
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{{Vspace}}
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<!--
 +
; R-code option
 +
:Submit code according to the following requirements. Make sure your code is documented.
 +
-->
  
 +
;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 [[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.
 +
:# When you are done, submit the link to your page via Quercus as described above
  
−
</div>
 
−
<div id="BIO">
 
 
== Contents ==
 
== Contents ==
−
<!-- included from "../components/BIN-PPI-Analysis.components.wtxt", section: "contents" -->
 
  
 
{{Task|1=
 
{{Task|1=
 
*Read the introductory notes on {{ABC-PDF|BIN-PPI-Analysis|the analysis of Protein-Protein Interaction (PPI) networks}}.
 
*Read the introductory notes on {{ABC-PDF|BIN-PPI-Analysis|the analysis of Protein-Protein Interaction (PPI) networks}}.
 
}}
 
}}
−
 
  
 
{{Vspace}}
 
{{Vspace}}
  
 +
{{ABC-unit|BIN-PPI-Analysis.R}}
  
 +
{{Vspace}}
  
−
==Working with biological graphs in R==
+
=== Optional: Cytoscape ===
−
 
 
−
{{task|1=
 
−
 
 
−
* Open RStudio.
 
−
* Choose File &rarr; Recent Projects &rarr; BCH441_2016.
 
−
* Pull the latest version of the project repository from GitHub.
 
−
* type <tt>init()</tt>
 
−
* Open the file <tt>BCH441_A11.R</tt> and work through the entire tutorial.
 
−
 
 
−
* At the end of the tutorial, you are being asked to print '''R''' code and data on a sheet of paper and bring this to class. This will be marked by me and worth maximally 4 marks. Be careful to follow the instructions exactly, especially regarding how to use your student number as a randomization seed.
 
−
 
 
−
}}
 
−
 
 
−
;This is all that is required. There is optional material below that you may find interesting.
 
−
 
 
−
{{Vspace}}
 
  
 +
{{Smallvspace}}
  
−
==Optional: Data visualization and analysis ==
+
;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.
  
 
{{task|1=
 
{{task|1=
Line 134: Line 136:
  
  
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==Visualizing Interactions==
 
−
 
−
 
−
'''[http://www.cytoscape.org/ Cytoscape]''' is a program originally written in Trey Ideker's lab at the [http://www.systemsbiology.org/ Institue for Systems Biology], that is now a thriving, open-source community project for the development of a biology-oriented network display and analysis tool.
 
−
 
−
 
−
{{#pmid:21063955}}
 
−
 
−
 
−
Cytoscape is now [http://cytoscape.org/ available as '''version 3'''] and should be straightforward to download and install.
 
−
 
−
<div class="reference-box">Cytoscape 3 tutorials <small>([http://opentutorials.cgl.ucsf.edu/index.php/Portal:Cytoscape3])</small>
 
−
* [http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Introduction_to_Cytoscape_3 Introduction to Cytoscape 3: User Interface]
 
−
* [http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Introduction_to_Cytoscape_3.1-part2 Introduction to Cytoscape 3.1: Part 2 - importing networks]
 
−
* [http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Introduction_to_Cytoscape_3-part3 Introduction to Cytoscape 3: Part 3 - Web import]
 
−
* [http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Filtering_and_Editing_in_Cytoscape_3 Cytoscape 3: Filtering and editing]
 
−
</div>
 
−
 
−
 
−
<div class="reference-box">Cytoscape tutorials <small>([http://wiki.cytoscape.org/Presentations/Basic])</small>
 
−
* Browse over the [http://wiki.cytoscape.org/Presentations/03_Download_Data Cytoscape Downloading Data tutorial]
 
−
* Work through the [http://irefindex.uio.no/wiki/iRefScape '''iRefScape''' &mdash; iRefIndex Cytoscape plugin tutorial:] Installation, data selection and use.
 
−
* Work through the [http://wiki.cytoscape.org/Presentations/04_Expression_Data Cytoscape Basic expression analysis tutorial]
 
−
 
−
{{#pmid:20926419}}
 
−
{{#pmid:21877285}}
 
−
</div>
 
−
 
−
<div class="reference-box">The [http://wiki.cytoscape.org/Welcome '''Cytoscape wiki''' and manual], and the [http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats Cytoscape manual page on '''network formats'''].</div>
 
−
;Platform
 
−
{{#pmid:14597658}}
 
−
{{#pmid:17947979}}
 
−
{{#pmid:19597788}}
 
−
{{#pmid:21149340}}
 
−
;Plugins
 
−
{{#pmid:20122237}}
 
−
{{#pmid:20926419}}
 
−
{{#pmid:21473782}}
 
−
{{#pmid:21975162}}
 
−
{{#pmid:22070249}}
 
−
</div>
 
−
 
−
 
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{{Vspace}}
 
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−
== Further reading, links and resources ==
 
−
<!-- {{#pmid: 19957275}} -->
 
−
<!-- {{WWW|WWW_GMOD}} -->
 
−
<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
 
−
 
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{{Vspace}}
 
−
 
−
 
−
== Notes ==
 
−
<!-- included from "../components/BIN-PPI-Analysis.components.wtxt", section: "notes" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "notes" -->
 
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<references />
 
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{{Vspace}}
 
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</div>
 
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<div id="ABC-unit-framework">
 
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== Self-evaluation ==
 
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<!-- included from "../components/BIN-PPI-Analysis.components.wtxt", section: "self-evaluation" -->
 
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<!--
 
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=== Question 1===
 
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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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<div class="about">
 
<div class="about">
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:2017-08-05
 
:2017-08-05
 
<b>Modified:</b><br />
 
<b>Modified:</b><br />
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:2017-08-05
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:2020-10-07
 
<b>Version:</b><br />
 
<b>Version:</b><br />
−
:0.1
+
: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
 
*0.1 First stub
 
*0.1 First stub
 
</div>
 
</div>
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[[Category:ABC-units]]
 
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<!-- included from "ABC-unit_components.wtxt", 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}}
 
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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"