Monday, October 29, 2013

Differentially expressed genes (fold_change >=2)

Title	Plot	Excel file
MAPlot of 158 genes (s4 vs. s1)	File:MAPlot-s1s4.pdf	File:Sig-genes-s1s4.xlsx
MAPlot of 240 genes (s7 vs. s1)	File:MAPlot-s1s7.pdf	File:Sig-genes-s1s7.xlsx

Friday, October 25, 2013

Comparison of 3 Samples with total mRNA (We debugged rows with multiple gene IDs)

Title	Plot	Plot (scaled by gene)	Excel file
Heatmap of 90 significant genes in 3 samples	File:Heatmap-90sig-genes-3sample.pdf	File:Heatmap-90sig-genes-3sample-scaled.pdf	File:Sig-genes-in-3samples-modi.xlsx

Comparison of 3 Samples with total mRNA

Title	Plot	Plot (scaled by gene)	Excel file
Heatmap of 89 significant genes in 3 samples	File:Heatmap-89sig-genes-3sample.pdf	File:Heatmap-89sig-genes-3sample-scaled.pdf	File:Sig genes-in-3samples.xlsx

mRNA export affected by KD or OE of nup211

Title	Plot
Export (C/N) of 40 genes affected by KD of nup211 (heatmap)	File:Heatmap-40genes-export-KD.pdf
Export (C/N) of 39 genes affected by OE of nup211 (heatmap)	File:Heatmap-39genes-export-OE.pdf

Comparison of 4 Samples with total mRNA

Title	Plot	Plot (scaled by gene)
Heatmap of 76 significant genes	File:Heatmap-76sig-genes-4sample.pdf	File:Heatmap-76sig-genes-4sample-scaled.pdf

Comparison of all 10 Samples

Title	Plot	Plot (scaled by gene)
Barplot Nup 211	File:Nup211.pdf
Heatmap of 13 genes of interest	File:Heatmap-13interested-genes-10sample.pdf
Heatmap of 80 significant genes	File:Heatmap-80sig-genes.pdf	File:Heatmap-80sig-genes-scaled-by-gene.pdf
Heatmap of 39 genes of interest	File:Heatmap-39interested-genes.pdf	File:Heatmap-39interested-genes-scaled-by-gene.pdf

Comparison between Samples 1,4,7, and 10

Title	Plots
Volcano Plots
Heatmap of 13 genes of interest	File:Heatmap-13interested-genes.pdf
Heatmap of 76 significant genes	File:Heatmap-76sig-genes.pdf

Trapnell et al (2012). Nature Protocol. 7(2): 562.
File:Texudo-pipeline-nprot.2012.016.pdf
PDF
Goff et al (2012). CummeRbund Manual
File:CummeRbund-manual.pdf