Taking 2022 gene count matrix through DESeq2 to enrichment with DAVID and revigo. Also, compared 2021 control vs exposed DEG list to the 2022 control vs exposed DEG list through to Revigo.

Notes

Some notes before getting into the details.

Something I’m unsure of is which result metric from DAVID to use to identify significantly enriched biological processes. Here’s the documentation from the DAVID webpage: https://david.ncifcrf.gov/content.jsp?file=functional_annotation.html#bonfer

2022 DEG lists Annotation –> Enrichment

R Code for DESeq2: paper-pycno-sswd-2021-2022/code/22-deseq2-2022.Rmd

R Code for Annotation: paper-pycno-sswd-2021-2022/code/23-annotating-deg-lists.Rmd

Control 6 vs exposed 6

6 controls (3 adults and 3 juveniles) vs 6 exposed (3 adults and 3 juveniles).

DEG list: paper-pycno-sswd-2021-2022/analyses/22-deseq2-2022/DEGlist_2022_controlVexposed.tab

6,237 DEGs.

PCA:

Volcano:

Heatmap of top 50 DEGs:

Annotation

DEG annotated list: paper-pycno-sswd-2021-2022/analyses/23-annotating-deg-lists/DEGlist_2022_exposedVcontrol_annotated.tab

Enrichment

DAVID output (with genome blast uniprot accession IDs as background):

paper-pycno-sswd-2021-2022/analyses/24-2021-2022-enrichment/DAVID-2022-controlVexposed.txt

Here’s the significantly enriched processes:
Are they most significant?? I did it based on Bonferroni/Fold Enrichment.

Term	Count	%	PValue	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR
GO:0006511~ubiquitin-dependent protein catabolic process	94	2.14758967	4.19E-08	4107	156	10742	1.57602717	2.97E-04	2.29E-04	2.29E-04
GO:0016567~protein ubiquitination	167	3.81539867	6.47E-08	4107	314	10742	1.3910645	4.58E-04	2.29E-04	2.29E-04
GO:0002181~cytoplasmic translation	32	0.73109436	4.64E-07	4107	40	10742	2.09242756	0.00328165	9.83E-04	9.82E-04
GO:0006508~proteolysis	194	4.43225954	5.55E-07	4107	383	10742	1.32483991	0.00392559	9.83E-04	9.82E-04

REVIGO

Here’s what I put into REVIGO: paper-pycno-sswd-2021-2022/analyses/24-2021-2022-enrichment/2022-controlVexposed-forREVIGO.txt. GO terms and p-values for those with p-value <0.05. 89 terms.

Treemap list:
paper-pycno-sswd-2021-2022/analyses/24-2021-2022-enrichment/2022-controlVexposed_Revigo_BP_TreeMap.tsv

Treemap:

Control vs Exposed taking Age into account

Control Adults (n=3)
Control Juveniles (n=3)
Exposed Adults (n=3)
Exposed Juveniles (n=3)

DEG list: paper-pycno-sswd-2021-2022/analyses/22-deseq2-2022/DEGlist_2022_controlVexposed_withAge.tab

6,202 DEGs.

Annotation

DEG annotated list: paper-pycno-sswd-2021-2022/analyses/23-annotating-deg-lists/DEGlist_2022_exposedVcontrol_withAge_annotated.tab

Enrichment

DAVID output with genome blast uniprot accession IDs as background):

paper-pycno-sswd-2021-2022/analyses/24-2021-2022-enrichment/DAVID-2022-controlVexposed-withage.txt

Here’s the significantly enriched processes:
Are they most significant?? I did it based on Bonferroni/Fold Enrichment.

Term	Count	%	PValue	List Total	Pop Hits	Pop Total	Fold Enrichment	Bonferroni	Benjamini	FDR
GO:0002181~cytoplasmic translation	34	0.77237619	1.40E-08	4137	40	10742	2.20708243	9.96E-05	9.96E-05	9.96E-05
GO:0006511~ubiquitin-dependent protein catabolic process	93	2.11267606	1.51E-07	4137	156	10742	1.54795374	0.00106954	4.98E-04	4.98E-04
GO:0016567~protein ubiquitination	166	3.77101318	2.10E-07	4137	314	10742	1.37270769	0.00149374	4.98E-04	4.98E-04
GO:0006508~proteolysis	193	4.38437074	1.66E-06	4137	383	10742	1.30845311	0.01172974	0.00294977	0.00294811
GO:0006412~translation	100	2.27169468	1.56E-05	4137	184	10742	1.41117802	0.10520751	0.02223252	0.02222001