View source for Spombe

=Friday, June 13, 2014=
Fold Change vs. Chrom Location Plots (batch 2)
* [http://borreliagenome.org/spombe/fc-chrm1.html Chromosome 1]
* [http://borreliagenome.org/spombe/fc-chrm2.html Chromosome 2]
* [http://borreliagenome.org/spombe/fc-chrm3.html Chromosome 3]
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=Wednesday, March 5, 2014=
MA Plots (batch 2)
* [http://borreliagenome.org/spombe/t1t2.html 10T vs. 558T]
* [http://borreliagenome.org/spombe/t1t3.html 13T vs. 558T]
Excel file: [[File:Sig-genes-batch2.xlsx|thumbnail]]
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=Sunday, January 5, 2014=
Interactive MA Plots (with Fc added in tooltips)
* [http://borreliagenome.org/spombe/maplot-s4s1-addFc.html s4 vs. s1]
* [http://borreliagenome.org/spombe/maplot-s7s1-addFc.html s7 vs. s1]
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=Monday, November 25, 2013=
Pathway analysis (fold_change >=1)
* Molecular Function (s4 vs. s1): [[File:S4s1-MF.svg|thumbnail]]
* Biological Process (s4 vs. s1): [[File:S4s1-BP.svg|thumbnail]]
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=Wednesday, November 13-14, 2013=
* Differentially expressed genes (fold_change >=1)
{| class="wikitable"
|-
! Interactive MA Plots || Excel file
|-
| [http://borreliagenome.org/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]]
|}


* Expression levels in cytosol & nuclei (fold_change of c/n ratio >= 1)
{| class="wikitable"
|-
! 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://borreliagenome.org/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)]
|}
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=Tuesday, November 12, 2013=
Interactive MA Plots
* [http://borreliagenome.org/spombe/maplot-s4s1-v1.html s4 vs. s1]
* [http://borreliagenome.org/spombe/maplot-s7s1-v1.html s7 vs. s1]
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=Tuesday, November 5, 2013=
Differentially expressed genes (fold_change >=2)
* s4 vs. s1, s7 vs.s1: [[File:Sig-genes-cut2.xlsx|thumbnail]]
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=Monday, November 4, 2013=
Linked plots for C/N ratio:
* Over-expression experiment: [[File:Linked-oe.svg|thumbnail]]
* Knock-down experiment: [[File:Linked-kd.svg|thumbnail]]
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=Sunday, November 3, 2013=
Interactive MA Plots for C/N ratios
* Strain s5/s6 vs. s2/s3: [[File:Maplot-cn-oe.svg|thumbnail]]
* Strain s8/s9 vs. s2/s3: [[File:Maplot-cn-kd.svg|thumbnail]]
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=Saturday, November 2, 2013=
Interactive MA Plots for total expression levels
* Strain s4 vs. s1: [[File:Maplot-s4s1.svg|thumbnail]]
* Strain s7 vs. s1: [[File:Maplot-s7s1.svg|thumbnail]]
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=Tuesday, October 30, 2013=
Gene export affected by OE or KD of nup211: Dotplot of C/N ratios of genes expression
{| class="wikitable"
|-
! Title !! Plot || Excel file
|-
| Strain s4 vs. s1 || [[File:Dotplot-cn-10.558.pdf|thumbnail]] || [[File:Ratio-cn-10.558.xlsx|thumbnail]]
|-
| Strain s7 vs. s1 || [[File:Dotplot-cn-13.558.pdf|thumbnail]] || [[File:Ratio-cn-13.558.xlsx|thumbnail]]
|}
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=Monday, October 29, 2013=
Differentially expressed genes (fold_change >=2)
{| class="wikitable"
|-
! Title !! Plot || Excel file
|-
| MAPlot of 158 genes (s4 vs. s1) || [[File:MAPlot-s1s4.pdf|thumbnail]] || [[File:Sig-genes-s1s4.xlsx|thumbnail]]
|-
| MAPlot of 240 genes (s7 vs. s1) || [[File:MAPlot-s1s7.pdf|thumbnail]] || [[File:Sig-genes-s7-s1.xlsx|thumbnail]]
|}
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=Friday, October 25, 2013=
Comparison of 3 Samples with total mRNA (We debugged rows with multiple gene IDs)
{| class="wikitable"
|-
! Title !! Plot || Plot (scaled by gene) || Excel file
|-
| Heatmap of 90 significant genes in 3 samples || [[File:Heatmap-90sig-genes-3sample.pdf|thumbnail]] || [[File:Heatmap-90sig-genes-3sample-scaled.pdf|thumbnail]] || [[File:Sig-genes-in-3samples-modi.xlsx|thumbnail]]
|}
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=Wednesday, October 23, 2013=
Comparison of 3 Samples with total mRNA
{| class="wikitable"
|-
! Title !! Plot || Plot (scaled by gene) || Excel file
|-
| Heatmap of 89 significant genes in 3 samples || [[File:Heatmap-89sig-genes-3sample.pdf|thumbnail]] || [[File:Heatmap-89sig-genes-3sample-scaled.pdf|thumbnail]] || [[File:Sig_genes-in-3samples.xlsx|thumbnail]]
|}
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=Thursday, October 17, 2013=
mRNA export affected by KD or OE of nup211
{| class="wikitable"
|-
! Title !! Plot
|-
| Export (C/N) of 40 genes affected by KD of nup211 (heatmap) || [[File:Heatmap-40genes-export-KD.pdf|thumbnail]]
|-
| Export (C/N) of 39 genes affected by OE of nup211 (heatmap) || [[File:Heatmap-39genes-export-OE.pdf|thumbnail]]
|}
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=Wednesday, October 16, 2013=
Comparison of 4 Samples with total mRNA
{| class="wikitable"
|-
! Title !! Plot || Plot (scaled by gene)
|-
| Heatmap of 76 significant genes || [[File:Heatmap-76sig-genes-4sample.pdf|thumbnail]] || [[File:heatmap-76sig-genes-4sample-scaled.pdf|thumbnail]]
|}
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=Friday, October 11, 2013=
Comparison of all 10 Samples
{| class="wikitable"
|-
! Title !! Plot || Plot (scaled by gene)
|-
| Barplot Nup 211 || [[File:Nup211.pdf|thumbnail]] ||  
|-
| Heatmap of 13 genes of interest || [[File:Heatmap-13interested-genes-10sample.pdf|thumbnail]] ||
|-
| Heatmap of 80 significant genes || [[File:Heatmap-80sig-genes.pdf|thumbnail]] || [[File:Heatmap-80sig-genes-scaled-by-gene.pdf|thumbnail]]
|-
| Heatmap of 39 genes of interest || [[File:Heatmap-39interested-genes.pdf|thumbnail]] || [[File:Heatmap-39interested-genes-scaled-by-gene.pdf|thumbnail]]
|}
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=Tuesday, October 8, 2013=
Comparison between Samples 1,4,7, and 10
{| class="wikitable"
|-
! Title !! Plots
|-
| Volcano Plots || [[File:Vocano-4-samples.png|left|100px]]
|-
| Heatmap of 13 genes of interest || [[File:Heatmap-13interested-genes.pdf|thumbnail]]
|-
| Heatmap of 76 significant genes || [[File:Heatmap-76sig-genes.pdf|thumbnail]]
|}
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=References=
* Trapnell et al (2012). Nature Protocol. 7(2): 562. [[File:Texudo-pipeline-nprot.2012.016.pdf|thumbnail|PDF]]
* Goff et al (2012). CummeRbund Manual [[File:CummeRbund-manual.pdf|thumbnail]]