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 |
Written on January 30, 2020