Things I realized were missing when I was updating methods and results

A real “bits and bobs” situation.

Integration analysis

Worked some InDesign magic (lol) and smashed some figures together. Not a fan of how the circos plot looks next to the WCNA output. I want to make the text larger and remove the temperature lines. I also wonder if I can just remove compound names that weren’t connected to something else. I’m going to have Ariana give me feedback on this figure so I can make it better.

Figure 1. Integration figure

Metabolomics ASCA

When I started writing the results, I realized I probably should perform enrichment for the PCs of interest. So, I did. All the output can be found in this folder. I opened the loadings names I saved and pasted them into MetaboAnalyst for Pathway Enrichment. I removed any duplicate names when needed. For name matching, I also looked into synonyms from PubChem where appropriate.

PC 1:

• Fixed 3-Aminopiperidine-2,6-dione (comma was removing the last part of the name)
• Enriched pathways
  • valine, leucine, and isoleucine biosynthesis (same as 13ºC vs. 30ºC at day 22 comparison!!): isoleucine, leucine, threonine
  • glutathione metabolism: cadaverine, putrescine, glycine, 5-oxoproline

PC 2:

• No significantly enriched pathways
• valine, leucine, and isoleucine biosynthesis was the top one but not significant

PC 3:

• No significantly enriched pathways
• tyrosine metabolism was the top one but not significant

PC4:

• Two significantly enriched pathways
  • arginine biosynthesis (top pathway but not enriched for 13ºC vs. 5ºC at day 22): 2-oxoglutarate, glutamate, citruline
  • phenylalanine, tyrosine, and tryptophan biosynthesis: phenylalanine, tyrosine

Lipidomics ASCA

I did the same thing with the lipidomics ASCA! The output can be found here.

PC 1:

• No enriched LION terms

PC 2:

• 11 enriched LION terms! Several related to glycerophospholipids, saturation state, etc.

Results figures

Of course I now had to go back into InDesign to figure out what to do with my results figures. I need to remove the WCNA information, add ASCA information, and add ASCA enrichment information (maybe). I started with the easier lift, which was to add the ASCA component information to the multipanel with the PLS-DA.

Figure 2. PLS-DA and ASCA multipanel

Now to figure out what to do with the enrichment information. I needed to add enrichment information from PCs 1 and 4 from the metabolomics ASCA and PC 2 from the lipidomics ASCA.

Figure 3. Enrichment information

So……….I’m not a huge fan of that figure. I am strongly contemplating moving it to the supplement.

Next step for me: get some feedback on my methods in writing group and start outlining the discussion (?!?!?!?!?!)

Going forward

1. Outline discussion
2. Write discussion
3. Outline introduction
4. Write introduction
5. Write abstract