Difference between revisions of "BIN-PPI-Concepts"

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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%;">
 
Protein-Protein Interaction (PPI) Concepts
 
Protein-Protein Interaction (PPI) Concepts
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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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(Detecting PPIs; the relationship abstraction; complexes, binary and n-ary interactions)
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</div>
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<div class="keywords">
 
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<b>Keywords:</b>&nbsp;
 
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Detecting PPIs; the relationship abstraction; complexes, binary and n-ary interactions
 
 
</div>
 
</div>
  
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{{Smallvspace}}
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__TOC__
 
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{{DEV}}
 
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{{Vspace}}
 
  
  
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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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<b>Abstract:</b><br />
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<section begin=abstract />
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This unit introduces concepts and methods of protein-protein interaction networks.
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<section end=abstract />
 
</div>
 
</div>
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<div id="ABC-unit-framework">
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<!-- ============================  -->
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== Abstract ==
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<hr>
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<!-- included from "../components/BIN-PPI-Concepts.components.wtxt", section: "abstract" -->
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<table>
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...
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<tr>
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<td style="padding:10px;">
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<b>Objectives:</b><br />
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This unit will ...
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* ... introduce the graph abstraction for interaction-type data;
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== This unit ... ==
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* ... explain methodologies for measuring protein-protein interactions.
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=== Prerequisites ===
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</td>
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<!-- included from "../components/BIN-PPI-Concepts.components.wtxt", section: "prerequisites" -->
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<td style="padding:10px;">
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<!-- included from "ABC-unit_components.wtxt", section: "notes-external_prerequisites" -->
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<b>Outcomes:</b><br />
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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:
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After working through this unit you ...
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<!-- included from "FND-prerequisites.wtxt", section: "bch" -->
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* ... are familar with the terminology in the field;
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<!-- included from "FND-prerequisites.wtxt", section: "biomolecules" -->
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* ... are aware of the distinction between pairwise interactions and interactions in complexes.
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</td>
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</tr>
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</table>
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<!-- ============================ -->
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<hr>
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<b>Deliverables:</b><br />
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<section begin=deliverables />
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<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>
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<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
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<section end=deliverables />
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<!-- ============================  -->
 +
<hr>
 +
<section begin=prerequisites />
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<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.
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<!-- 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.
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<!-- 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.
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<!-- included from "FND-prerequisites.wtxt", section: "central_dogma" -->
 
 
*<b>The Central Dogma</b>: Regulation of transcription and translation; protein biosynthesis and degradation; quality control.
 
*<b>The Central Dogma</b>: Regulation of transcription and translation; protein biosynthesis and degradation; quality control.
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<!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" -->
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This unit builds on material covered in the following prerequisite units:<br />
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You need to complete the following units before beginning this one:
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*[[BIN-SYS-Concepts|BIN-SYS-Concepts (Systems Models)]]
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*[[BIN-SYS-Concepts]]
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<section end=prerequisites />
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*[[FND-MAT-Graphs_and_networks]]
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<!-- ============================  -->
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</div>
  
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{{Smallvspace}}
  
  
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=== Objectives ===
 
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<!-- included from "../components/BIN-PPI-Concepts.components.wtxt", section: "objectives" -->
 
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...
 
  
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{{Smallvspace}}
  
  
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=== Outcomes ===
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__TOC__
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<!-- included from "../components/BIN-PPI-Concepts.components.wtxt", section: "outcomes" -->
 
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...
 
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=== Deliverables ===
 
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<!-- included from "../components/BIN-PPI-Concepts.components.wtxt", section: "deliverables" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-time_management" -->
 
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*<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.
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-journal" -->
 
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*<b>Journal</b>: Document your progress in your [[FND-Journal|course journal]].
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-insights" -->
 
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*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|insights! page]].
 
  
 
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=== Evaluation ===
 
=== Evaluation ===
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<!-- included from "../components/BIN-PPI-Concepts.components.wtxt", section: "evaluation" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "eval-none" -->
 
 
<b>Evaluation: NA</b><br />
 
<b>Evaluation: NA</b><br />
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:This unit is not evaluated for course marks.
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<div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div>
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<div id="BIO">
 
 
== Contents ==
 
== Contents ==
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<!-- included from "../components/BIN-PPI-Concepts.components.wtxt", section: "contents" -->
 
 
{{Task|1=
 
{{Task|1=
 
*Read the introductory notes on {{ABC-PDF|BIN-PPI-Concepts|the concepts behind the measurement and analysis of protein-protein interactions}}.
 
*Read the introductory notes on {{ABC-PDF|BIN-PPI-Concepts|the concepts behind the measurement and analysis of protein-protein interactions}}.
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== Further reading, links and resources ==
 
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<!-- {{#pmid: 19957275}} -->
 
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<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
 
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== Notes ==
 
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<!-- included from "../components/BIN-PPI-Concepts.components.wtxt", section: "notes" -->
 
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<references />
 
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== Self-evaluation ==
 
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=== Question 1===
 
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Question ...
 
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Answer ...
 
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Answer ...
 
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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">
 
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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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:2017-11-09
 
<b>Version:</b><br />
 
<b>Version:</b><br />
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:0.1
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:1.0
 
<b>Version history:</b><br />
 
<b>Version history:</b><br />
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*1.0 First live version
 
*0.1 First stub
 
*0.1 First stub
 
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Latest revision as of 05:46, 23 September 2020

Protein-Protein Interaction (PPI) Concepts

(Detecting PPIs; the relationship abstraction; complexes, binary and n-ary interactions)


 


Abstract:

This unit introduces concepts and methods of protein-protein interaction networks.

Objectives:
This unit will ...

  • ... introduce the graph abstraction for interaction-type data;
  • ... explain methodologies for measuring protein-protein interactions.

Outcomes:
After working through this unit you ...

  • ... are familar with the terminology in the field;
  • ... are aware of the distinction between pairwise interactions and interactions in complexes.

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.
    • The Central Dogma: Regulation of transcription and translation; protein biosynthesis and degradation; quality control.

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


     



     



     


    Evaluation

    Evaluation: NA

    This unit is not evaluated for course marks.

    Contents

    Task:


     



     


    About ...
     
    Author:

    Boris Steipe <boris.steipe@utoronto.ca>

    Created:

    2017-08-05

    Modified:

    2017-11-09

    Version:

    1.0

    Version history:

    • 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-Concepts&oldid=11613"