Sarah Carratt 4.12.11: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
No edit summary |
No edit summary |
||
Line 16: | Line 16: | ||
**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 10:00, 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