Difference between revisions of "FND-PPI-Physical vs genetic"

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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%;">
 
Physical- vs. Genetic Interactions
 
Physical- vs. Genetic Interactions
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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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(The fundamental difference between physical and “genetic” interactions. Topology of pathways.)
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<b>Keywords:</b>&nbsp;
 
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The fundamental difference between physical and “genetic” interactions. Topology of pathways.
 
 
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</div>
  
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__TOC__
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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 discusses how "genetic interactions" are measured and can be used to infer pathway topologies.
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<!-- ============================  -->
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<table>
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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 concept of "genetic interactions";
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* ... illustrate how the interpretation of genetic interactions can be used to analyze pathway topologies.
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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 concept of '''genetic interactions''', and how they are fundamentally different from '''physical interactions'''.
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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>
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<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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<!-- ============================  -->
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<hr>
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<section begin=prerequisites />
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<b>Prerequisites:</b><br />
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This unit builds on material covered in the following prerequisite units:<br />
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*[[BIN-PPI-Concepts|BIN-PPI-Concepts (Protein-Protein Interaction (PPI) Concepts)]]
  
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<section end=prerequisites />
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<!-- ============================  -->
 
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== Abstract ==
 
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...
 
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== This unit ... ==
 
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=== Prerequisites ===
 
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<!-- included from "../components/FND-PPI-Physical_vs_genetic.components.wtxt", section: "prerequisites" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" -->
 
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You need to complete the following units before beginning this one:
 
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*[[BIN-PPI-Concepts]]
 
  
  
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=== Objectives ===
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__TOC__
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<!-- included from "../components/FND-PPI-Physical_vs_genetic.components.wtxt", section: "objectives" -->
 
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...
 
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=== Outcomes ===
 
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...
 
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=== Deliverables ===
 
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<!-- included from "../components/FND-PPI-Physical_vs_genetic.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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<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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== Contents ==
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Genetic interactions are '''very''' different from physicl interactions. Here the word ''interaction'' is used in an entirely different sense: it is not synonymous with ''contact'' it is synonymous with ''influence''. In fact, most proteins that display genetic interactions would '''not''' be expected to interact physically as well. (Why? Think.) It is important not to mix up the two.
  
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To understand what genetic interactions imply, think of the following analogy. If I were to break the wrist of my right arm, my survival would probably not be affected. My left arm would provide sufficient redundancy for most tasks.  What about breaking the right index finger, or spraining the elbow as well? Painful, but functionally not much worse than breaking the wrist alone. What about indigestion, bunyons, cancer, or Alzheimers in addition to the fracture? Annoying, but really not significantly more so with or without a broken wrist. What about a broken left wrist? That would be bad. Losing the function of both hands is much, much worse than losing the function of only one hand. This is the kind of functional ordering that genetic interactions achieve: if two genes are active in the '''same''' system (like the right wrist and index finger) they will '''not''' display genetic interaction. The pathway is blocked and it matters little whether it is blocked in one or two points. If two genes work in completely '''different''' systems, they will also '''not''' show genetic interactions (like a fracture, combined with indigestion). Only if two genes affect parallel, mutually redundant pathways (left and right arm) will their joint deletion cause a critical situation for the affected organism. If the organism dies, we call this a ''synthetic lethal'' effect.
  
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Genetic interactions can be observed in high-throughput experiments that systematically explore all pairs of gene-deletions in an organism, and the results provide insight how pathways can be topologically ordered according to shared objectives!
  
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== Contents ==
 
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<!-- included from "../components/FND-PPI-Physical_vs_genetic.components.wtxt", section: "contents" -->
 
  
 
{{Task|1=
 
{{Task|1=
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* Read the introductory notes on {{ABC-PDF|FND-PPI-Physical_vs_genetic|the difference between physical- and genetic "interactions"}} and its significance.
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* Read the introductory notes on {{ABC-PDF|FND-PPI-Physical_vs_genetic|the concepts of genetic "interactions", how they are interpreted, and how they are fundamentally different from physical interactions.}}
 
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== Further reading, links and resources ==
 
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== Notes ==
 
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== Self-evaluation ==
 
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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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:2017-08-05
 
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<b>Version:</b><br />
 
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*1.0 First live
 
*0.1 First stub
 
*0.1 First stub
 
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Latest revision as of 06:00, 23 September 2020

Physical- vs. Genetic Interactions

(The fundamental difference between physical and “genetic” interactions. Topology of pathways.)


 


Abstract:

This unit discusses how "genetic interactions" are measured and can be used to infer pathway topologies.

Objectives:
This unit will ...

  • ... introduce the concept of "genetic interactions";
  • ... illustrate how the interpretation of genetic interactions can be used to analyze pathway topologies.

Outcomes:
After working through this unit you ...

  • ... are familar with the concept of genetic interactions, and how they are fundamentally different from physical interactions.

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



     



     



     


    Evaluation

    Evaluation: NA

    This unit is not evaluated for course marks.

    Contents

    Genetic interactions are very different from physicl interactions. Here the word interaction is used in an entirely different sense: it is not synonymous with contact it is synonymous with influence. In fact, most proteins that display genetic interactions would not be expected to interact physically as well. (Why? Think.) It is important not to mix up the two.

    To understand what genetic interactions imply, think of the following analogy. If I were to break the wrist of my right arm, my survival would probably not be affected. My left arm would provide sufficient redundancy for most tasks. What about breaking the right index finger, or spraining the elbow as well? Painful, but functionally not much worse than breaking the wrist alone. What about indigestion, bunyons, cancer, or Alzheimers in addition to the fracture? Annoying, but really not significantly more so with or without a broken wrist. What about a broken left wrist? That would be bad. Losing the function of both hands is much, much worse than losing the function of only one hand. This is the kind of functional ordering that genetic interactions achieve: if two genes are active in the same system (like the right wrist and index finger) they will not display genetic interaction. The pathway is blocked and it matters little whether it is blocked in one or two points. If two genes work in completely different systems, they will also not show genetic interactions (like a fracture, combined with indigestion). Only if two genes affect parallel, mutually redundant pathways (left and right arm) will their joint deletion cause a critical situation for the affected organism. If the organism dies, we call this a synthetic lethal effect.

    Genetic interactions can be observed in high-throughput experiments that systematically explore all pairs of gene-deletions in an organism, and the results provide insight how pathways can be topologically ordered according to shared objectives!


    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
    • 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=FND-PPI-Physical_vs_genetic&oldid=11614"