Shelly’s Notebook: Fri. April 5, 2019 Oyster Seed Proteomics

Re-do analysis with updated selected proteins from clustering without day 0.

Kaitlin’s previous clustering analysis included day 0. She made a euclidean distance matrix and cut the dendrogram at 250 to ID 33 proteins in 35 different clusters.

In the new analysis, she made a euclidean distance matrix and cut the dendrogram at 150 to ID 135 proteins in 61 different clusters.

There are now 135 protiens ID’d by clustering, 143 proteins ID’d by ASCA, and 163 proteins ID’d by proportions test to be significantly influenced by temperature.

I made a new proportional venn diagram in R to show proteins commonly and uniquely identified by different statistical methods. img

I also made a new heatmap of these proteins. img

These figures will be the new figure 3 in the manuscript.

I also plotted heatmaps and abundance line plots of proteins identified by each individual method as a way to verify the methods are selecting proteins that have abundances affected by temperature. To see these, CHECK OUT THIS MARKDOWN FILE FOR NEW FIGURES

Markdown file was generated by this R markdown file, so it out if you’re interested in the R code.

Still need to:

  1. Re-run the GO analysis/cytoscape with updated protein list generated today
  2. dig into the last figure in terms of what the biological significance actually is
  3. work on the discussion

from shellytrigg

Grace’s Notebook: Annotated Protein List from MS Stats with set thresholds… in progress

Yesterday and today I got some more 2015 DIA paper-related tasks done, including making a table that includes the proteins detected above a log2FC of 3.00 and below -3.00, and one that was annotated…

Tasks completed

  1. Uploaded the skyline daily .zip file to the Roberts Lab PanoramaWeb in a new folder entitled “2015-DIA-Cgigas-seed”.
  2. Updated links in the GitHub paper-pacific.oyster-larvae/protocols

Threshold protein lists

R script

Yesterday I made one without annotation. 20190403-2015Cgseed-protcomp.csv 26 proteins.

Today I made one with Steven’s annotated protein list. 20 proteins.

We cross-referenced the 20190403-2015Cgseed-protcomp.csv with Steven’s pivot table created from 0403-DIA-Cgseed.csv and determined that if the log2FC number is negative, it’s 23C, and if the log2FC is positive, it’s 29C.

Weekend and next week tasks

  1. Keep working on paper (intro, methods, discussion)
  2. Get results for the paper figured out- do I include the phenotype data even though the 29C data is pooled from 7 silos…?
  3. Get repository to the point where it only has the important information. I still think I have too much stuff in there. But once everything is finished, it’ll be easier to ID what needs to stay and what needs to go.

from Grace’s Lab Notebook