Sarah Carratt 4.12.11

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**time 1 graphed vs time 2...dot plot!
**time 1 graphed vs time 2...dot plot!
**two+ clusters that are distinct, separate based on where they fall..."an art"
**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

Revision as of 13:00, 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
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