Differential expression and dosage compensation in RNAseq – NGS2015

Dr. Chris Hamm, University of Kansas, side effects of sexual reproduction in Lepidoptera!

2015-08-27_01-24-34

Explanation of ESA, species status dependent # of self-sustaining populations, Mitchell’s satyr butterfly endangered. Suggests Butterfly People.

K-means cluster plots, each vertical bar individual. Michigan different than other populations.

Diversification of Lepidoptera, Mutanen et al. 2010:

2015-08-27_01-46-16

Evolution of sex chromosomes: female heterogamety, “chocoblock full of transposable elements” Sex chromosomes present gene dosage problem, no matter how many chromosomes you have, you still have the same gene expression. Females mammals inactivate extra X chromosome. Drosophila males double expression to deal with balance.

Tutorial

https://angus.readthedocs.org/en/2015/_static/SLDC-code.html
https://github.com/ngs-docs/angus/blob/2015/week3/SLDC/SLDC-code.Rmd

Simulated Data

plot_Code

MA

Practice Data

Bmori.dat <- read.csv(“Bmori-data.csv”, header = TRUE)

4plots

Plotting in R – Awesome Digression!

Multiple plots on one space, add plots, text, arrows, whatever on top with base R.
Reset with:

par(mfrow=c(1,1))

RPKM

Looking at expression per chromosome:

expr

zchrom

MA plots

http://web.mit.edu/~r/current/arch/i386_linux26/lib/R/library/limma/html/plotma.html
I posted a question on the Bioconductor listserv:

https://support.bioconductor.org/p/71562/
http://nar.oxfordjournals.org/content/43/7/e47

limma::plotMA

weird_MAplot

plot(log2(res1_filtered$baseMean), res1_filtered$log2FoldChange, col=ifelse(res1_filtered$padj < 0.25, “red”,”gray67″),main=”In vivo, ApoE vs. WT (padj<0.25)”,xlim=c(1,20),ylim=c(-10,10),pch=20,cex=1)
abline(h=c(-1 ,1), col=”blue”)

MAplot_invivo_DKOvWT_June2015

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About Lisa Cohen

PhD student at UC Davis.
This entry was posted in Genomics Workshop. Bookmark the permalink.

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