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 took the next steps to perform this across all samples, as well as generate some comparison plots. After this, will explore how spurious transcription relates to methylation levels across genes.

See 65-exon-coverage.qmd for code.

Note

Code and plots link to commit 585fb03.

Plots

All plots are line plots of the mean natural log fold-change in exon expression (Exons 2-6), relative to Exon 1. 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.