Sarah Carratt 4.12.11: Difference between revisions
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**POSITIVE!!! (duh) | **POSITIVE!!! (duh) | ||
*'''Production Functions''' | *'''Production Functions''' | ||
**(A) Linear | '''**(A) Linear | ||
***a +bx | ***a +bx | ||
**(B) Michaelis-Menten | **(B) Michaelis-Menten | ||
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***approximates a switch | ***approximates a switch | ||
***on-off + transition | ***on-off + transition | ||
''' |
Revision as of 10:34, 12 April 2011
Sources for this Week
- Oltvai & Barabasi (2002) Science
- Lee et al. (2002) Science
- Harbison et al. (2004) Nature
- MacIsaac et al. (2006) BMC Bioinformatics
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
- 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
Production
- Production goes up in presence of x2
- Move x2 means higher rate
- What does the graph look like?
- POSITIVE!!! (duh)
- Production Functions
**(A) Linear
- a +bx
- (B) Michaelis-Menten
- Vx/(K+x)
- (C) Sigmoidal
- approximates a switch
- on-off + transition