Sarah Carratt 4.12.11

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(Clustering)
(Functions)
Line 38: Line 38:
**Produce less
**Produce less
**Decrease in production rate
**Decrease in production rate
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 +
==Network Picture==
 +
*Takes the matrix to cartoon land
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*Provides qualitative information about production
 +
*All arrows are about production
 +
*Does the arrow = activation or production?
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*Degradation=decrease contrary to production
 +
 +
==Degradation==
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*Production - Degradation
 +
*Half life is measure of degradation (time of how long it takes half of a sample to degrade)
 +
*Pure degradation modul
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*x = quantity at time t
 +
*dx/dt = -λ·x(t)
 +
**λ=fraction of quantity degraded in unit of time (units = 1/time)
 +
*Start with fixed amount, X = x(0)
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*x(t) = e<sup>-λt</sup>X

Revision as of 13:14, 12 April 2011

Contents

Gene Regulation and Modeling

  • Focused on measuring RNA and modeling dynamic behavior of proteins that RNA spins off
  • High activity in RNA should mean high protein behavior
  • Low activity in RNA should mean low protein behavior

Modeling in Network Construction

  • Qualitative, not just quantitative/numbers
  • Active genes working simultaneously → transcription factors
    • Define "simultaneously"
  • Database represents a model built through experiments and literature

Clustering

  • Define distance metric (this is what it means for two things to be close together)
  • Easily build matrix of closeness once distance is defined
  • Clustering is more subtle
    • time 1 graphed vs time 2...dot plot!
    • two+ clusters that are distinct, separate based on where they fall..."an art"

Matrices

  • 1's and 0's
  • Changes in G1 produces changes in G3 if that box is 1
  • Arrows in diagram show effector/affectee relationship
  • Called an adjacency matrix → graph theory
  • Graph theory is a way to put structures to pictures?
  • When handed adjacency matrix...which ways do the arrows go?

Functions

  • How does quantity of protein present relate to genes?
  • Do we know if relationships are activation or repression?
    • Back to microarrays...up or down?
  • What does activation mean?
    • Positive log fold change
    • Produce more/Do more
    • Increase in rate of change (production = rate↑)
  • What does repression mean?
    • Negative log fold change
    • Slow, stop, reduce synthesis/activity
    • Produce less
    • Decrease in production rate

Network Picture

  • Takes the matrix to cartoon land
  • Provides qualitative information about production
  • All arrows are about production
  • Does the arrow = activation or production?
  • Degradation=decrease contrary to production

Degradation

  • Production - Degradation
  • Half life is measure of degradation (time of how long it takes half of a sample to degrade)
  • Pure degradation modul
  • x = quantity at time t
  • dx/dt = -λ·x(t)
    • λ=fraction of quantity degraded in unit of time (units = 1/time)
  • Start with fixed amount, X = x(0)
  • x(t) = e-λtX
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