GOAL:
To use the NEXTFLOW and deseq2 results to get differential gene expression patterns.

1. Between 25C and 37C within a variety. How many genes? A list of them. How much over lap btw the 4 plant varieties (upsetR)?
2. All genes at 37C each variety.
3. Heatmap like Anthony made in their paper.

Original request is below:

Right now, we have the following data:
Heinz 25C expression patterns & numbers in each path
Heinz 37C expression patterns & numbers in each path
Malintka 25C expression patterns & numbers in each path
Malintka 37C expression patterns & numbers in each path
Nagcarlang 25C expression patterns & numbers in each path
Nagcarlang 37C expression patterns & numbers in each path
Tamaulipas 25C expression patterns & numbers in each path
Tamaulipas 37C expression patterns & numbers in each path

The main things I want to do are:
Find genes that change significantly in both 25C and 37C for each cultivar
Then, we can compare expression patterns to see if they are changing in the same directions
Find genes that are significantly changing only in the 37C condition for each cultivar
Essentially "subtracting" the genes that are also changing at 25C so we are left with uniquely changing 37C genes
Make a heat map of these genes like Figure 13D in Anthony's paper, where each cultivar and temp is on the x-axis (8 sections with 2 time points each = 16 columns to show gene expression levels), and genes are on the y-axis.
This heat map could be made for only the genes significantly changing for all temps/time points/cultivars, and another heat map could be made for the ones only significantly changing in all three thermotolerant lines, but not Heinz
If there are too many genes, we could try to create a "cutoff" with the "Max_PP" section?
Would these things be possible to do? I know Gloria's data did not previously account for temperature, so if there is a better way to visualize the data, I am open to other methods.

If you would like to meet about these things, I am also happy to find a time to talk this over with you. Please let me know what you think.

Thanks so much!

Best,
Kelsey