Spombe

Friday, June 13, 2014

Fold Change vs. Chrom Location Plots (batch 2)

• Chromosome 1
• Chromosome 2
• Chromosome 3

Wednesday, March 5, 2014

MA Plots (batch 2)

• 10T vs. 558T
• 13T vs. 558T

Excel file:

File:Sig-genes-batch2.xlsx

Sunday, January 5, 2014

Interactive MA Plots (with Fc added in tooltips)

• s4 vs. s1
• s7 vs. s1

Monday, November 25, 2013

Pathway analysis (fold_change >=1)

• Molecular Function (s4 vs. s1):
  File:S4s1-MF.svg
• Biological Process (s4 vs. s1):
  File:S4s1-BP.svg

Wednesday, November 13-14, 2013

• Differentially expressed genes (fold_change >=1)

Interactive MA Plots	Excel file
s4 vs. s1	File:Genes-s4s1.xlsx
s7 vs. s1	File:Genes-s7s1.xlsx

• Expression levels in cytosol & nuclei (fold_change of c/n ratio >= 1)

Interactive Plots	Excel file
Strain 10 vs. 558 (78 genes)	File:Exp-cn-10.558.xlsx
Strain 13 vs. 558 (83 genes)	File:Exp-cn-13.558.xlsx
Strains 10, 13, and 558 (78+83-30=131 genes)

Tuesday, November 12, 2013

Interactive MA Plots

• s4 vs. s1
• s7 vs. s1

Tuesday, November 5, 2013

Differentially expressed genes (fold_change >=2)

• s4 vs. s1, s7 vs.s1:
  File:Sig-genes-cut2.xlsx

Monday, November 4, 2013

Linked plots for C/N ratio:

• Over-expression experiment:
  File:Linked-oe.svg
• Knock-down experiment:
  File:Linked-kd.svg

Sunday, November 3, 2013

Interactive MA Plots for C/N ratios

• Strain s5/s6 vs. s2/s3:
  File:Maplot-cn-oe.svg
• Strain s8/s9 vs. s2/s3:
  File:Maplot-cn-kd.svg

Saturday, November 2, 2013

Interactive MA Plots for total expression levels

• Strain s4 vs. s1:
  File:Maplot-s4s1.svg
• Strain s7 vs. s1:
  File:Maplot-s7s1.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 s4 vs. s1	File:Dotplot-cn-10.558.pdf	File:Ratio-cn-10.558.xlsx
Strain s7 vs. s1	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