Laura’s Notebook: Oly DMG analysis, Jan. 30th, 2020

Today I identified 46 differentially methylated genes among two Olympia oyster populations, Hood Canal and South Sound. This was performed using a binomial GLM and Chi-square tests. The script was adapted from Hollie Putnam’s script (/hputnam/Geoduck_Meth/master/RAnalysis/Scripts/GM.Rmd), which may have been adopted from the Lieu et al. 2018 paper .

The analysis was performed in a RMarkdown notebook, please see that here: 09-DMG-analysis

Here are the GO terms associated with genes of known function. Some notes:
– 18 out of the 46 genes were annotated with GO terms
– 9 out of the 46 genes were annotated but did not have associated GO terms (may have to find those manually …)
– 19 out of the 46 genes were of unknown function

term ID description frequency pin? log10 p-value uniqueness dispensability
GO:0006468 protein phosphorylation 4.137 % -3.7877 0.40 0.00
GO:0006807 nitrogen compound metabolic process 38.744 % -2.2764 0.78 0.03
GO:0006207 ‘de novo’ pyrimidine nucleobase biosynthetic process 0.192 % -2.2764 0.46 0.06
GO:0006281 DNA repair 2.234 % -2.4853 0.50 0.20
GO:0006030 chitin metabolic process 0.077 % -1.6311 0.49 0.21
GO:0006520 cellular amino acid metabolic process 5.591 % -2.2764 0.42 0.35
GO:0006412 translation 5.686 % -2.4853 0.28 0.55
GO:0016567 protein ubiquitination 0.523 % -1.4336 0.44 0.56

image

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