Updates on paper methods and results. Updates on goals.

notes:

Met with Steven to go through paper methods –> streamlining, simplifying, and organizing.

Still more to do –> will go through and make sure things are accurate first, then will simplify.

Things to add to paper:

  • Results: alignment rates for libraries I’m talking about

Met with Drew to give an update about what I’ve been up to, and what my goals are.

Some important things she wants to see in the paper:

  • clearer results –> decoding the genes and what they mean (will get at this next week with results finalizations, and the following week with discussion)
  • Clear hypotheses
  • Clear statements about how juveniles and adults show no difference - that was really new information for the sea star group

Annotating DEG Lists with GO BP terms:

https://github.com/grace-ac/paper-pycno-sswd-2021-2022/blob/main/code/23-annotating-deg-lists.Rmd

Summer 2021

https://github.com/grace-ac/paper-pycno-sswd-2021-2022/blob/main/analyses/23-annotating-deg-lists/DEGlist_2021_exposedVcontrol_annotated.tab

Summer 2022

https://github.com/grace-ac/paper-pycno-sswd-2021-2022/blob/main/analyses/23-annotating-deg-lists/DEGlist_2022_exposedVcontrol_annotated.tab

https://github.com/grace-ac/paper-pycno-sswd-2021-2022/blob/main/analyses/23-annotating-deg-lists/DEGlist_2022_exposedVcontrol_withAge_annotated.tab

https://github.com/grace-ac/paper-pycno-sswd-2021-2022/blob/main/analyses/23-annotating-deg-lists/DEGlist_2022_exposedVcontrol_withAgeContrast_annotated.tab

Comparing 2021 and 2022

https://github.com/grace-ac/paper-pycno-sswd-2021-2022/blob/main/code/25-compare-2021-2022.Rmd

Unique 2021

https://github.com/grace-ac/paper-pycno-sswd-2021-2022/blob/main/analyses/25-compare-2021-2022/DEGlist_unique_2021.tab

Unique 2022

https://github.com/grace-ac/paper-pycno-sswd-2021-2022/blob/main/analyses/25-compare-2021-2022/DEGlist_unique_2022.tab

Shared 2021 and 2022

https://github.com/grace-ac/paper-pycno-sswd-2021-2022/blob/main/analyses/25-compare-2021-2022/DEGlist_same_2021-2022.tab

Get list of genes from shared DAVID output

R code: https://github.com/grace-ac/paper-pycno-sswd-2021-2022/blob/main/code/25-compare-2021-2022.Rmd

shared DEG list DAVID enrichment output: https://github.com/grace-ac/paper-pycno-sswd-2021-2022/blob/main/analyses/24-2021-2022-enrichment/2021-2022-same-DAVID.txt

Want the genes that are associated with the top 9 processes (<0.05 Benjamini-Hochberg corrected p-values).

Term Count % PValue List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR
GO:0043161~proteasome-mediated ubiquitin-dependent protein catabolic process 80 2.67558528 1.86E-08 2807 173 10742 1.7696469 1.11E-04 1.11E-04 1.11E-04
GO:0002181~cytoplasmic translation 28 0.93645485 4.77E-08 2807 40 10742 2.67880299 2.84E-04 1.42E-04 1.42E-04
GO:0006508~proteolysis 144 4.81605351 5.96E-07 2807 383 10742 1.43881996 0.00354188 9.63E-04 9.61E-04
GO:0006511~ubiquitin-dependent protein catabolic process 70 2.34113712 6.47E-07 2807 156 10742 1.71718141 0.00384429 9.63E-04 9.61E-04
GO:0007229~integrin-mediated signaling pathway 26 0.86956522 1.52E-05 2807 44 10742 2.2613272 0.08674616 0.01814814 0.01811463
GO:0033209~tumor necrosis factor-mediated signaling pathway 17 0.56856187 3.58E-05 2807 24 10742 2.7106935 0.19197353 0.03508708 0.03502229
GO:0042742~defense response to bacterium 31 1.0367893 4.12E-05 2807 59 10742 2.0107238 0.2177764 0.03508708 0.03502229
GO:0006412~translation 73 2.44147157 6.75E-05 2807 184 10742 1.51826567 0.33111824 0.04711885 0.04703184
GO:0097352~autophagosome maturation 20 0.66889632 7.12E-05 2807 32 10742 2.39178839 0.34563155 0.04711885 0.04703184

Use the uniprot accession ID list to get the genes… but how. Is it literally going to be the same as if I were to use the GO ID and get all those genes?

GitHub Issue: 1996. Saw that there’s been a response but didn’t get around to it today, will give it a look soon!