Spombe: Difference between revisions

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=Friday, June 13, 2014=
Fold Change vs. Chrom Location Plots (batch 2)
* [http://borreliabase.org/~wgqiu/spombe/fc-chrm1.html Chromosome 1]
* [http://borreliabase.org/~wgqiu/spombe/fc-chrm2.html Chromosome 2]
* [http://borreliabase.org/~wgqiu/spombe/fc-chrm3.html Chromosome 3]
<br>
=Wednesday, March 5, 2014=
MA Plots (batch 2)
* [http://borreliabase.org/~wgqiu/spombe/t1t2.html 10T vs. 558T]
* [http://borreliabase.org/~wgqiu/spombe/t1t3.html 13T vs. 558T]
Excel file: [[File:Sig-genes-batch2.xlsx|thumbnail]]
<br>
<br>
=Sunday, January 5, 2014=
Interactive MA Plots (with Fc added in tooltips)
* [http://borreliabase.org/~wgqiu/spombe/maplot-s4s1-addFc.html s4 vs. s1]
* [http://borreliabase.org/~wgqiu/spombe/maplot-s7s1-addFc.html s7 vs. s1]
<br>
=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]]
<br>
=Wednesday, November 13-14, 2013=
* Differentially expressed genes (fold_change >=1)
{| class="wikitable"
|-
! Interactive MA Plots || Excel file
|-
| [http://borreliabase.org/~wgqiu/spombe/maplot-s4s1.html s4 vs. s1] || [[File:Genes-s4s1.xlsx|thumbnail]]
|-
| [http://borreliabase.org/~wgqiu/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://borreliabase.org/~wgqiu/spombe/cn-oe.html Strain 10 vs. 558 (78 genes)] || [[File:Exp-cn-10.558.xlsx|thumbnail]]
|-
| [http://borreliabase.org/~wgqiu/spombe/cn-kd.html Strain 13 vs. 558 (83 genes)] || [[File:Exp-cn-13.558.xlsx|thumbnail]]
|-
| [http://borreliabase.org/~wgqiu/spombe/cn-3strains.html Strains 10, 13, and 558 (78+83-30=131 genes)]
|}
<br>
=Tuesday, November 12, 2013=
Interactive MA Plots
* [http://borreliabase.org/~wgqiu/spombe/maplot-s4s1-v1.html s4 vs. s1]
* [http://borreliabase.org/~wgqiu/spombe/maplot-s7s1-v1.html s7 vs. s1]
<br>
=Tuesday, November 5, 2013=
Differentially expressed genes (fold_change >=2)
* s4 vs. s1, s7 vs.s1: [[File:Sig-genes-cut2.xlsx|thumbnail]]
<br>
=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]]
<br>
=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]]
<br>
=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]]
<br>
=Tuesday, October 30, 2013=
=Tuesday, October 30, 2013=
Gene export affected by OE or KD of nup211: Dotplot of C/N ratios of genes expression
Gene export affected by OE or KD of nup211: Dotplot of C/N ratios of genes expression
Line 5: Line 86:
! Title !! Plot || Excel file
! Title !! Plot || Excel file
|-
|-
| Strain 10 vs. 558 || [[File:Ma.svg|thumbnail]] || (Clickable SVG graph with links to [http://www.pombase.org/ PomBase]
| Strain s4 vs. s1 || [[File:Dotplot-cn-10.558.pdf|thumbnail]] || [[File:Ratio-cn-10.558.xlsx|thumbnail]]
|-
|-
| Strain 10 vs. 558 || [[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]]
|-
| Strain 13 vs. 558 || [[File:Dotplot-cn-13.558.pdf|thumbnail]] || [[File:Ratio-cn-13.558.xlsx|thumbnail]]
|}
|}
<br>


=Monday, October 29, 2013=
=Monday, October 29, 2013=
Line 17: Line 97:
|-
|-
! Title !! Plot || Excel file
! Title !! Plot || Excel file
|-
| MAPlot of 158 genes (s4 vs. s1) || [[File:Ma.svg|thumbnail]] || (SVG graph: download & mouseover to view gene names)
|-
|-
| MAPlot of 158 genes (s4 vs. s1) || [[File:MAPlot-s1s4.pdf|thumbnail]] || [[File:Sig-genes-s1s4.xlsx|thumbnail]]
| MAPlot of 158 genes (s4 vs. s1) || [[File:MAPlot-s1s4.pdf|thumbnail]] || [[File:Sig-genes-s1s4.xlsx|thumbnail]]
Line 24: Line 102:
| MAPlot of 240 genes (s7 vs. s1) || [[File:MAPlot-s1s7.pdf|thumbnail]] || [[File:Sig-genes-s7-s1.xlsx|thumbnail]]
| MAPlot of 240 genes (s7 vs. s1) || [[File:MAPlot-s1s7.pdf|thumbnail]] || [[File:Sig-genes-s7-s1.xlsx|thumbnail]]
|}
|}
<br>


=Friday, October 25, 2013=
=Friday, October 25, 2013=
Line 33: Line 112:
| 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]]
| 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]]
|}
|}
<br>


=Wednesday, October 23, 2013=
=Wednesday, October 23, 2013=
Line 42: Line 122:
| 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]]
| 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]]
|}
|}
<br>


=Thursday, October 17, 2013=
=Thursday, October 17, 2013=
Line 53: Line 134:
| Export (C/N) of 39 genes affected by OE of nup211 (heatmap) || [[File:Heatmap-39genes-export-OE.pdf|thumbnail]]
| Export (C/N) of 39 genes affected by OE of nup211 (heatmap) || [[File:Heatmap-39genes-export-OE.pdf|thumbnail]]
|}
|}
<br>


=Wednesday, October 16, 2013=
=Wednesday, October 16, 2013=
Line 62: Line 144:
| Heatmap of 76 significant genes || [[File:Heatmap-76sig-genes-4sample.pdf|thumbnail]] || [[File:heatmap-76sig-genes-4sample-scaled.pdf|thumbnail]]
| Heatmap of 76 significant genes || [[File:Heatmap-76sig-genes-4sample.pdf|thumbnail]] || [[File:heatmap-76sig-genes-4sample-scaled.pdf|thumbnail]]
|}
|}
<br>


=Friday, October 11, 2013=
=Friday, October 11, 2013=
Line 77: Line 160:
| Heatmap of 39 genes of interest || [[File:Heatmap-39interested-genes.pdf|thumbnail]] || [[File:Heatmap-39interested-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]]
|}
|}
<br>


=Tuesday, October 8, 2013=
=Tuesday, October 8, 2013=
Line 90: Line 174:
| Heatmap of 76 significant genes || [[File:Heatmap-76sig-genes.pdf|thumbnail]]
| Heatmap of 76 significant genes || [[File:Heatmap-76sig-genes.pdf|thumbnail]]
|}
|}
<br>


=References=
=References=
* Trapnell et al (2012). Nature Protocol. 7(2): 562. [[File:Texudo-pipeline-nprot.2012.016.pdf|thumbnail|PDF]]
* 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]]
* Goff et al (2012). CummeRbund Manual [[File:CummeRbund-manual.pdf|thumbnail]]

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:

File:Sig-genes-batch2.xlsx



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
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


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
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
Vocano-4-samples.png
Heatmap of 13 genes of interest
File:Heatmap-13interested-genes.pdf
Heatmap of 76 significant genes
File:Heatmap-76sig-genes.pdf


References

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