Here is a paper related to this topic.

It has a few of the names we want as it relates to quercetin biosynthesis.

https://www.sciencedirect.com/science/article/pii/S0304423818304679

Planning for group meeting presentation today:

• RR makes a presentation in google drive
• team adds to and edits it

Notes from meeting:

• Shiny app that would provide a pathway chooser which would know the genes associated with the pathway and show the expression levels (heat map) from a given dataset of those genes.
• Work with James Pease Lab to determine Annotation work needed or provide our own smaller version instead from tomato group only

Presentation was made.
Lengthy discussion ensued !!

Copy of the presentation can be found here:
https://docs.google.com/presentation/d/1kWJnZlbsW6SElp9TH1gaY4x8F-zIJKskN98Y6iIzFzs/edit?usp=drive_link

We found out about Jame's MASSIVE annotation efforts. He shared with us his massive spread sheet, where each tab is a gene classification of some sort.
He has BUSCO scores for the tomato orthologs that match the BUSCO genes.

Jame's Google sheet of anotations:

https://docs.google.com/spreadsheets/d/1NFqsAPT394mmkLCI9eAFYK798Ym0UfSIWpjRCs9bdQU/edit?usp=sharing

Sent email to Muday lab and our internal group:

Hello all,

This is mainly a question for Muday lab. Do you think you would be available or interested in taking on the following task?

It would be nice to investigate how or if enzymes involved in flavonoid biosynthesis are differentially expressed in response to the heat stress treatment. To do that, it would help if we knew which annotated gene models might encode these enzymes. If we knew that, we could very easily test for over- or under-enrichment of these genes in the DE gene set.

To do this, we would need something like this:

An xlsx (MS Excel) spreadsheet document with columns:

• enzyme acronym (e.g., CHS, F3'5'H, FNS)
• longer name of the enzyme / enzymatic activity
• SL4 gene name

Having a spreadsheet listing gene names encoding flavonoid biosynthetic genes would be useful for running statistical tests of enrichment for this pathway.

If you are available and interested in taking this on, the best place to start in my view is probably going to be the following file, which lists all SL4 gene names and gene descriptions:

• https://bitbucket.org/hotpollen/flavonoid-rnaseq/src/main/ExternalDataSets/S_lycopersicum_Sep_2019.bed.gz

This file is a tab-delimited file where each row indicates a different gene model. The next-to-last column (column 13) lists SL4 gene name and the final column (column 14) lists SL4 gene description.

Hopefully we can discuss this Friday!

-Ann

Follow-up: Muday lab let us know that they have a list of these but are not ready to share it with us because they have a few new things to add.
Doing no further work on this pending updates from them.

Decided not to do this due to lack of enthusiasm from Muday Lab.