Info

General info:

  • Differential expression analysis using deseq2.
  • Some values have been rounded

Datasets analysed:

  • mirna smrnaseq: TRUE
  • mirna excerpt: TRUE
  • pirna excerpt: FALSE
  • trna excerpt: TRUE
  • circrna excerpt: FALSE
  • gencode excerpt: TRUE

Treatment comparisons:

  • treatment1 - treatment2
  • treatment1 - treatment3

Total number of samples: 12

Number of samples in each treatment group:

  • treatment1: 4
  • treatment2: 4
  • treatment3: 4

MA plots

These plots plot the log2 fold changes versus the mean of normalized counts. These can be used to visualize the differences between treatment group comparisons. In general we would expect the expression of RNA’s to remain consistent between treatment groups and so the MA plot should be similar to the shape of a trumpet with most points residing on a y intercept of 0. Differentially expressed RNA’s are marked blue.

RNA’s with a p-value smaller than 0.1 and a log fold change greater/smaller than +-log2(1.1) are plotted here.

Blue: RNA’s with an adjusted p-value smaller than 0.1 and a log fold change greater/smaller than +-log2(1.1)

Red: RNA’s with an adjusted p-value smaller than 0.1 and a log fold change greater/smaller than +-log2(1.1)

Yellow: RNA’s with an adjusted p-value smaller than 0.05 and a log fold change greater/smaller than +-log2(1.1)

Green: RNA’s with an adjusted p-value smaller than 0.01 and a log fold change greater/smaller than +-log2(1.1)

treatment1 - treatment2

miRNA’s (smrnaseq)

miRNA’s (excerpt)

tRNA’s (excerpt)

gencodes (excerpt)

treatment1 - treatment3

miRNA’s (smrnaseq)

miRNA’s (excerpt)

tRNA’s (excerpt)

gencodes (excerpt)

 

Generated by ESR Genomics

www.esr.cri.nz