Spombe: Difference between revisions

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=Friday, June 13, 2014=
=Friday, June 13, 2014=
Fold Change vs. Chrom Location Plots (batch 2)
Fold Change vs. Chrom Location Plots (batch 2)
* [http://diverge.hunter.cuny.edu/spombe/fc-chrm1.html Chromosome 1]
* [http://borreliabase.org/~wgqiu/spombe/fc-chrm1.html Chromosome 1]
* [http://diverge.hunter.cuny.edu/spombe/fc-chrm2.html Chromosome 2]
* [http://borreliabase.org/~wgqiu/spombe/fc-chrm2.html Chromosome 2]
* [http://diverge.hunter.cuny.edu/spombe/fc-chrm3.html Chromosome 3]
* [http://borreliabase.org/~wgqiu/spombe/fc-chrm3.html Chromosome 3]
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=Wednesday, March 5, 2014=
=Wednesday, March 5, 2014=
MA Plots (batch 2)
MA Plots (batch 2)
* [http://diverge.hunter.cuny.edu/spombe/t1t2.html 10T vs. 558T]
* [http://borreliabase.org/~wgqiu/spombe/t1t2.html 10T vs. 558T]
* [http://diverge.hunter.cuny.edu/spombe/t1t3.html 13T vs. 558T]
* [http://borreliabase.org/~wgqiu/spombe/t1t3.html 13T vs. 558T]
Excel file: [[File:Sig-genes-batch2.xlsx|thumbnail]]
Excel file: [[File:Sig-genes-batch2.xlsx|thumbnail]]
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=Sunday, January 5, 2014=
=Sunday, January 5, 2014=
Interactive MA Plots (with Fc added in tooltips)
Interactive MA Plots (with Fc added in tooltips)
* [http://diverge.hunter.cuny.edu/spombe/maplot-s4s1-addFc.html s4 vs. s1]
* [http://borreliabase.org/~wgqiu/spombe/maplot-s4s1-addFc.html s4 vs. s1]
* [http://diverge.hunter.cuny.edu/spombe/maplot-s7s1-addFc.html s7 vs. s1]
* [http://borreliabase.org/~wgqiu/spombe/maplot-s7s1-addFc.html s7 vs. s1]
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! Interactive MA Plots || Excel file
! Interactive MA Plots || Excel file
|-
|-
| [http://borreliagenome.org/spombe/maplot-s4s1.html s4 vs. s1] || [[File:Genes-s4s1.xlsx|thumbnail]]
| [http://borreliabase.org/~wgqiu/spombe/maplot-s4s1.html s4 vs. s1] || [[File:Genes-s4s1.xlsx|thumbnail]]
|-
|-
| [http://borreliagenome.org/spombe/maplot-s7s1.html s7 vs. s1] || [[File:Genes-s7s1.xlsx|thumbnail]]
| [http://borreliabase.org/~wgqiu/spombe/maplot-s7s1.html s7 vs. s1] || [[File:Genes-s7s1.xlsx|thumbnail]]
|}
|}


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! Interactive Plots || Excel file
! Interactive Plots || Excel file
|-
|-
| [http://borreliagenome.org/spombe/cn-oe.html Strain 10 vs. 558 (78 genes)] || [[File:Exp-cn-10.558.xlsx|thumbnail]]
| [http://borreliabase.org/~wgqiu/spombe/cn-oe.html Strain 10 vs. 558 (78 genes)] || [[File:Exp-cn-10.558.xlsx|thumbnail]]
|-
|-
| [http://borreliagenome.org/spombe/cn-kd.html Strain 13 vs. 558 (83 genes)] || [[File:Exp-cn-13.558.xlsx|thumbnail]]
| [http://borreliabase.org/~wgqiu/spombe/cn-kd.html Strain 13 vs. 558 (83 genes)] || [[File:Exp-cn-13.558.xlsx|thumbnail]]
|-
|-
| [http://borreliagenome.org/spombe/cn-3strains.html Strains 10, 13, and 558 (78+83-30=131 genes)]
| [http://borreliabase.org/~wgqiu/spombe/cn-3strains.html Strains 10, 13, and 558 (78+83-30=131 genes)]
|}
|}
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=Tuesday, November 12, 2013=
=Tuesday, November 12, 2013=
Interactive MA Plots
Interactive MA Plots
* [http://borreliagenome.org/spombe/maplot-s4s1-v1.html s4 vs. s1]
* [http://borreliabase.org/~wgqiu/spombe/maplot-s4s1-v1.html s4 vs. s1]
* [http://borreliagenome.org/spombe/maplot-s7s1-v1.html s7 vs. s1]
* [http://borreliabase.org/~wgqiu/spombe/maplot-s7s1-v1.html s7 vs. s1]
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Latest revision as of 20:18, 27 March 2023

Friday, June 13, 2014

Fold Change vs. Chrom Location Plots (batch 2)


Wednesday, March 5, 2014

MA Plots (batch 2)

Excel file:



Sunday, January 5, 2014

Interactive MA Plots (with Fc added in tooltips)


Monday, November 25, 2013

Pathway analysis (fold_change >=1)


Wednesday, November 13-14, 2013

  • Differentially expressed genes (fold_change >=1)
Interactive MA Plots Excel file
s4 vs. s1
s7 vs. s1


  • Expression levels in cytosol & nuclei (fold_change of c/n ratio >= 1)
Interactive Plots Excel file
Strain 10 vs. 558 (78 genes)
Strain 13 vs. 558 (83 genes)
Strains 10, 13, and 558 (78+83-30=131 genes)


Tuesday, November 12, 2013

Interactive MA Plots


Tuesday, November 5, 2013

Differentially expressed genes (fold_change >=2)


Monday, November 4, 2013

Linked plots for C/N ratio:


Sunday, November 3, 2013

Interactive MA Plots for C/N ratios


Saturday, November 2, 2013

Interactive MA Plots for total expression levels


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
Strain s7 vs. s1


Monday, October 29, 2013

Differentially expressed genes (fold_change >=2)

Title Plot Excel file
MAPlot of 158 genes (s4 vs. s1)
MAPlot of 240 genes (s7 vs. s1)


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


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


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)
Export (C/N) of 39 genes affected by OE of nup211 (heatmap)


Wednesday, October 16, 2013

Comparison of 4 Samples with total mRNA

Title Plot Plot (scaled by gene)
Heatmap of 76 significant genes


Friday, October 11, 2013

Comparison of all 10 Samples

Title Plot Plot (scaled by gene)
Barplot Nup 211
Heatmap of 13 genes of interest
Heatmap of 80 significant genes
Heatmap of 39 genes of interest


Tuesday, October 8, 2013

Comparison between Samples 1,4,7, and 10

Title Plots
Volcano Plots
Vocano-4-samples.png
Heatmap of 13 genes of interest
Heatmap of 76 significant genes


References