Spombe

Saturday, November 2, 2013

Interactive MA Plots

Title	Plot
Strain s4 vs. s1	File:Maplot-s4s1.svg
Strain s7 vs. s1	File:Maplot-s4s1.svg Tuesday, October 30, 2013 Gene export affected by OE or KD of nup211: Dotplot of C/N ratios of genes expression Title Plot Excel file Strain 10 vs. 558 File:Dotplot-cn-10.558.pdf File:Ratio-cn-10.558.xlsx Strain 13 vs. 558 File:Dotplot-cn-13.558.pdf File:Ratio-cn-13.558.xlsx 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-s7-s1.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 Wednesday, October 23, 2013 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 Thursday, October 17, 2013 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 Wednesday, October 16, 2013 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 Friday, October 11, 2013 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 Tuesday, October 8, 2013 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 References 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