Question: Gene ontology comparsion between up- and down-regulated genes
2
gravatar for seta
3.0 years ago by
seta1.2k
Sweden
seta1.2k wrote:

Hi all friends,

I did differential expression analysis of an RNA-seq project. Then, using agrigo (enter link description here), I got enriched GO terms for up- and down-regulated genes, separately. Now, I was wondering how to statistically compare these GO terms between up and down regulated genes and show the results on the graph?

Thank you

ADD COMMENTlink modified 2.6 years ago by asanchez20 • written 3.0 years ago by seta1.2k
2

Option 1:

Try to present in this way, instead of microarray and RNAseq you can use up and downregulated category.

Figure source from Supplementary Figure 4. http://www.nature.com/ncomms/2015/150724/ncomms8743/extref/ncomms8743-s1.pdf

enter image description here

OR

Option 2:

http://genescf.kandurilab.org/ftp/GeneSCF-Documentation_v1.1.pdf

Page 12 (ggplot2 bubble plot)

OR

Option 3:

If you do not want to show number or percentage of genes appeared in each term, you can use simple double bar graph (up and down) with log10(Pvalue).

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by EagleEye6.4k

Thank you very much for your prompt response. The option 1 is great, but this is my first experience. Could you please help me out how I can draw a graph similar to this graph?

ADD REPLYlink written 3.0 years ago by seta1.2k

It is bit tricky to explain, but I will try my best.

1 Make your GO for up and downregulated as simple table

GO_name <tab> log10(p)_UP <tab>  log10(p)_DOWN <tab> UP_genes <tab> DOWN_genes

GO1 <tab> xx <tab> xx <tab> xx <tab> xx
GO2 <tab> xx <tab> NA* <tab> xx <tab> NA*

*NA represents not enriched in one of the category

2 Make heatmap for the log10 pvalue columns in the table using R heatmap.2

3 Make bar graph for the number of genes columns in the table using barplot

4 Use Inkscape (FREE) / Adobe Illustrator to place bar graph over heatmap.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by EagleEye6.4k

Many thanks for your explanation. I'll try it. Just one thing about GeneSCF that you also suggested, as I mentioned in my post, I have enriched GO terms for up and down-regulated genes. Would you please let me know if I just show them, without doing any statistical analysis (because I did it before) by this tool?

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by seta1.2k

It is better to show or present it with proper statistics. This will gain more confidence in your data. And for your information GeneSCF provides results with extensive statistical analysis.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by EagleEye6.4k
2
gravatar for asanchez
2.6 years ago by
asanchez20
asanchez20 wrote:

Hello I have just found this post You might consider using the goProfiles Bioconductor package (http://www.bioconductor.org/packages/release/bioc/html/goProfiles.html) whic is precisely intended to compare two gene lists based on their annotations at a geiven GO level. I am the maintainer of the package so feel free to ask any question if you want

ADD COMMENTlink written 2.6 years ago by asanchez20
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