Intro

As part of the CEABIGR project (GitHub repo) Steven performed some inital data wrangling to test out the basic calculations to determine the natural log of the fold change in exon expression, relative to Exon 1, for each gene in a single sample. The decision to perform the calculation in this manner was based on (Li et al. 2018). I plotted the results previously (on 20240103), but that did not include any sort of “normalization” across samples. Further discussion (GitHub Issue) decided to set a threshold based on the sum of reads for Exons 1 -6 per gene, per sample. The value decided on was a minimum sum of 10 reads for Exons 1-6, per gene, across all samples. E.g. If S13M has a sum of 15 reads for Exons 1-6 for a given gene, but S9M only has a sum of 8 reads for Exons 1-6 for that same gene, then that gene is discarded from the fold chane calculations.

This threshold filtering retained 23,101 genes (out of 38,264; 60.4% of genes)

After this, will explore how spurious transcription relates to methylation levels across genes, using this new exon sum threshold.

See 65-exon-coverage.qmd for code.

Note

Code and plots link to commit 0b9a89a.

Plots

All plots are line plots of the mean natural log fold-change in exon expression (Exons 2-6), relative to Exon 1. All genes used in the analysis had to Black bars represent standard error.

Note

Plots are simply arranged side-by-side. Scales of axes are not intended to match.

Line plots of mean natural log fold-change of exon expression relative to Exon 1. Pink line is control females. Blue line is control males. Black bars represent standard error.

Line plots of mean natural log fold-change of exon expression relative to Exon 1. Pink line is control females. Blue line is exposed females. Black bars represent standard error.

Line plots of mean natural log fold-change of exon expression relative to Exon 1. Pink line is control males. Blue line is exposed males. Black bars represent standard error.

Line plots of mean natural log fold-change of exon expression relative to Exon 1. Pink line is controls. Blue line is exposed. Black bars represent standard error.

Line plots of mean natural log fold-change of exon expression relative to Exon 1. Pink line is exposed females. Blue line is exposed males. Black bars represent standard error.

Line plots of mean natural log fold-change of exon expression relative to Exon 1. Pink line is females. Blue line is males. Black bars represent standard error.

References

Li, Yong, Yi Jin Liew, Guoxin Cui, Maha J. Cziesielski, Noura Zahran, Craig T. Michell, Christian R. Voolstra, and Manuel Aranda. 2018. “DNA Methylation Regulates Transcriptional Homeostasis of Algal Endosymbiosis in the Coral Model Aiptasia.” Science Advances 4 (8). https://doi.org/10.1126/sciadv.aat2142.