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 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 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
 
 
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__TOC__
 
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<div id="ABC-unit-framework">
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<div style="font-size:118%;">
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== Abstract ==
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<b>Abstract:</b><br />
 
<section begin=abstract />
 
<section begin=abstract />
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<!-- included from "./components/BIN-PPI-Concepts.components.txt", section: "abstract" -->
 
 
This unit introduces concepts and methods of protein-protein interaction networks.
 
This unit introduces concepts and methods of protein-protein interaction networks.
 
<section end=abstract />
 
<section end=abstract />
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</div>
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<!-- ============================  -->
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<hr>
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== This unit ... ==
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=== Prerequisites ===
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<td style="padding:10px;">
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<!-- included from "./components/BIN-PPI-Concepts.components.txt", section: "prerequisites" -->
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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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* ... explain methodologies for measuring protein-protein interactions.
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</td>
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<td style="padding:10px;">
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<b>Outcomes:</b><br />
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After working through this unit you ...
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* ... are familar with the terminology in the field;
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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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<!-- included from "./data/ABC-unit_components.txt", 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 "./data/ABC-unit_components.txt", section: "deliverables-journal" -->
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*<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.
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<!-- included from "./data/ABC-unit_components.txt", 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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<section end=deliverables />
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<!-- ============================  -->
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<hr>
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<section begin=prerequisites />
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<b>Prerequisites:</b><br />
 
<!-- included from "./data/ABC-unit_components.txt", section: "notes-external_prerequisites" -->
 
<!-- 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:
 
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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*<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.
 
<!-- included from "./data/ABC-unit_components.txt", section: "notes-prerequisites" -->
 
<!-- included from "./data/ABC-unit_components.txt", section: "notes-prerequisites" -->
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You need to complete the following units before beginning this one:
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This unit builds on material covered in the following prerequisite units:
 
*[[BIN-SYS-Concepts|BIN-SYS-Concepts (Systems Models)]]
 
*[[BIN-SYS-Concepts|BIN-SYS-Concepts (Systems Models)]]
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<section end=prerequisites />
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<!-- ============================  -->
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{{Smallvspace}}
  
  
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=== Objectives ===
 
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<!-- included from "./components/BIN-PPI-Concepts.components.txt", section: "objectives" -->
 
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This unit will ...
 
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* ... introduce the graph abstraction for interaction-type data;
 
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* ... explain methodologies for measuring protein-protein interactions.
 
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{{Vspace}}
 
  
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{{Smallvspace}}
  
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=== Outcomes ===
 
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<!-- included from "./components/BIN-PPI-Concepts.components.txt", section: "outcomes" -->
 
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After working through this unit you ...
 
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* ... are familar with the terminology in the field;
 
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* ... are aware of the distinction between pairwise interactions and interactions in complexes.
 
  
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{{Vspace}}
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__TOC__
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=== Deliverables ===
 
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<!-- included from "./components/BIN-PPI-Concepts.components.txt", section: "deliverables" -->
 
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<!-- included from "./data/ABC-unit_components.txt", 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.
 
−
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-journal" -->
 
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*<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.
 
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<!-- included from "./data/ABC-unit_components.txt", 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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== Contents ==
 
== Contents ==
 
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== Further reading, links and resources ==
 
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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.txt", section: "notes" -->
 
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<references />
 
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== Self-evaluation ==
 
== Self-evaluation ==
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=== Question 1===
 
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== Notes ==
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<!-- included from "./data/ABC-unit_components.txt", section: "notes" -->
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<references />
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== Further reading, links and resources ==
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<!-- {{#pmid: 19957275}} -->
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<!-- {{WWW|WWW_GMOD}} -->
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<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
  
 
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Revision as of 19:32, 26 January 2018

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:


 



 



 


Contents

Task:


 


Self-evaluation

Notes

Further reading, links and resources

 



 

If in doubt, ask! 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.


 

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

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