Sarah Carratt 4.12.11: Difference between revisions
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==Clustering== | ==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 | *Easily build matrix of closeness once distance is defined | ||
*Clustering is more subtle | *Clustering is more subtle | ||
Revision as of 10:01, 12 April 2011
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
