Spombe: Difference between revisions
Jump to navigation
Jump to search
imported>Lia |
mNo edit summary |
||
| (23 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
=Wednesday, November 13, 2013= | =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) | * Differentially expressed genes (fold_change >=1) | ||
{| class="wikitable" | {| class="wikitable" | ||
| Line 5: | Line 32: | ||
! Interactive MA Plots || Excel file | ! Interactive MA Plots || Excel file | ||
|- | |- | ||
| [http:// | | [http://borreliabase.org/~wgqiu/spombe/maplot-s4s1.html s4 vs. s1] || [[File:Genes-s4s1.xlsx|thumbnail]] | ||
|- | |- | ||
| [http:// | | [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" | {| class="wikitable" | ||
|- | |- | ||
! Interactive | ! Interactive Plots || Excel file | ||
|- | |- | ||
| [http:// | | [http://borreliabase.org/~wgqiu/spombe/cn-oe.html Strain 10 vs. 558 (78 genes)] || [[File:Exp-cn-10.558.xlsx|thumbnail]] | ||
|- | |- | ||
| [http:// | | [http://borreliabase.org/~wgqiu/spombe/cn-kd.html Strain 13 vs. 558 (83 genes)] || [[File:Exp-cn-13.558.xlsx|thumbnail]] | ||
|- | |- | ||
| [http:// | | [http://borreliabase.org/~wgqiu/spombe/cn-3strains.html Strains 10, 13, and 558 (78+83-30=131 genes)] | ||
|} | |} | ||
<br> | <br> | ||
| Line 26: | Line 53: | ||
=Tuesday, November 12, 2013= | =Tuesday, November 12, 2013= | ||
Interactive MA Plots | Interactive MA Plots | ||
* [http:// | * [http://borreliabase.org/~wgqiu/spombe/maplot-s4s1-v1.html s4 vs. s1] | ||
* [http:// | * [http://borreliabase.org/~wgqiu/spombe/maplot-s7s1-v1.html s7 vs. s1] | ||
<br> | <br> | ||
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)
- Molecular Function (s4 vs. s1):
- Biological Process (s4 vs. s1):
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)
- s4 vs. s1, s7 vs.s1:
Monday, November 4, 2013
Linked plots for C/N ratio:
- Over-expression experiment:
- Knock-down experiment:
Sunday, November 3, 2013
Interactive MA Plots for C/N ratios
- Strain s5/s6 vs. s2/s3:
- Strain s8/s9 vs. s2/s3:
Saturday, November 2, 2013
Interactive MA Plots for total expression levels
- Strain s4 vs. s1:
- Strain s7 vs. s1:
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 |  |
| Heatmap of 13 genes of interest | |
| Heatmap of 76 significant genes |
References
- Trapnell et al (2012). Nature Protocol. 7(2): 562.
- Goff et al (2012). CummeRbund Manual