Sarah Carratt 4.12.11

(Difference between revisions)
 Revision as of 13:14, 12 April 2011 (view source) (→Functions)← Previous diff Revision as of 13:21, 12 April 2011 (view source) (→Degradation)Next diff → Line 55: Line 55: *Start with fixed amount, X = x(0) *Start with fixed amount, X = x(0) *x(t) = e-λtX *x(t) = e-λtX + *d/dt(e-λt) = -λe-λtX + *dx/dt(e-λt) = -λe-λtX + *Half life = tH + **x(0) = X + **x(tH)= 1/2X = e-λtHX + **1/2= e-λtH + **2= eλtH + **λ=log(2)/tH + ***ln of 2 ≈ 0.69 + **tH = ln(2)/λ

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?

• Half life is measure of degradation (time of how long it takes half of a sample to degrade)
• x = quantity at time t
• dx/dt = -λ·x(t)
• λ=fraction of quantity degraded in unit of time (units = 1/time)
• x(t) = e-λtX
• d/dt(e-λt) = -λe-λtX
• dx/dt(e-λt) = -λe-λtX
• Half life = tH
• x(0) = X
• x(tH)= 1/2X = e-λtHX
• 1/2= e-λtH
• 2= eλtH
• λ=log(2)/tH
• ln of 2 ≈ 0.69
• tH = ln(2)/λ