RESULTS AND DISCUSSION
Result1: [SHS1]
In terms of breadth of responses, tThere are two patterns[SHS2]of domain families that highly response to biotic and abiotic conditions. One is only overrepresented in one condition; the other has a general response to stress conditions. There are more domain families that response to one abiotic stress, while there are more domain families which responses to more biotic stress. (The heat map will be included in the supplement[SHS3])
By doing a Fisher exact test, asterisk shows the differnces between biotic and abiotic response is significant[SHS4]
Q: What about breadth of responsiveness on a per gene basis? Can we do some perumulation test to show if the distribution is random? Talk about this first.
Q: One question is if the distrubtions shown above is expected randomly. So you can randomly sample genes/conditions to generate a nulll distribution for comparison.
Result 2 The function change in the external branches
2.1 More than half of the up or down response to stress condition of the ancestor gene are kept in the daughter gene. Along the time, the function change increased[SHS5].
Q: compared this to random expectation.
2.2 The lost of up responsiveness[SHS6] increase with time, and became saturatedafter Ks is more than 1.0.
Q: How is functional lost calculated?
The gain and lost rate for each condition can be put in the supplement[SHS7]
Emphasize:
1)Categories that involve functional changes have an overall increase as Ks increases.
- How about gain (NC-up or dn) vs. loss (Up or Dn to NC)?
For above, show down overall as well. Generate a supplement with all condition/time.
Fit the points with a logrithmic function, then calculate rates at ks=0.2 and ks=1
What's the above figure tell us? Why does it look so uneven compared to functional lost?
We need to talk about stochasticity in the estimates for gain.
Result 3
3.1 For the recently[SHS8]duplicated gene pairs, more than 70% of the up responsiveness of their ancestor gene went through partition.
Per condition partition vs. both_kept and may be look at this over a Ks range.
3.2 The partition rate varies for different families.[SHS9] There are more function partition happened in LRR and kinase families, while there are more functional conservatione in AP2 gene families. (fisher exact test for each families)
Q: So does TFs tend to have both kept??
Result 4:
The function partition after duplication is extremely asymmetric. No matter how many up responsiveness regulated conditions?? the ancestor gene have, only one daughter gene get most of function of its ancestor.
MATERIALS AND METHODS
[SHS1]Result heading
[SHS2]Not really two patterns since the distribution is continuous not bimodal.
[SHS3]Should show heatmap as a second part of this figure. Figure axes not labeled.
[SHS4]Does it make sense to compare between abiotic and biotic stress conditions??
[SHS5]In what direction? What have increased? Which kinds of functional changes?
[SHS6]Not for down? Also, need to change A, T, G to Up, Dn, NC in the figures. Figure axes not labeled.
[SHS7]Put supplement files together in a word file then.
[SHS8]What's the definition of "recent"?
[SHS9]Very interesting. So do you have a distribution of partition rates among families? Also, why is kinase not shown in the figure?