Question: Plotting A Pie-Chart Of Molecular Function Using Gene Ontology Method?
1
gravatar for J.F.Jiang
6.9 years ago by
J.F.Jiang720
China
J.F.Jiang720 wrote:

Hello, every Biostar user: In papers related with GO explanation, a beautiful pie-chart graph always came out to elucidate the molecular function enrichment distribution (percentage). And some papers mentioned that the pie-chart was produced by DAVID system.

Here, i got 200 gene symbols without any p-value or expression data. When i put the gene symbols into DAVID as gene list, I only got the classification of each GO component but can not find the place to draw a pie-chart graph.

And i tried several other softwares with failure because of the need of exprssion data or p value.

So, how can i get this picture by using those gene symbols only? Is there any webserver or softwares for this calculation?

Thank you!

gene • 14k views
ADD COMMENTlink modified 6.7 years ago by Khader Shameer17k • written 6.9 years ago by J.F.Jiang720
1

please upload an example of what you are talking about

ADD REPLYlink written 6.9 years ago by Jeremy Leipzig18k
4
gravatar for Ian
6.9 years ago by
Ian5.3k
University of Manchester, UK
Ian5.3k wrote:

There are a couple of tools that give interesting displays of GO term analyses:

CateGOrizer

REViGO (not a pie chart, but interesting display)

ADD COMMENTlink written 6.9 years ago by Ian5.3k
2
gravatar for Caddymob
6.9 years ago by
Caddymob930
United States
Caddymob930 wrote:

Some truth from the R pie chart man page:

"Pie charts are a very bad way of displaying information. The eye is good at judging linear measures and bad at judging relative areas. A bar chart or dot chart is a preferable way of displaying this type of data.

pie {graphics}

ADD COMMENTlink written 6.9 years ago by Caddymob930

Thank you for your comment. But is there any tools or softwares that can do this ontology enrichment and then give the pie-chart figure?

ADD REPLYlink written 6.9 years ago by J.F.Jiang720
0
gravatar for Khader Shameer
6.8 years ago by
Manhattan, NY
Khader Shameer17k wrote:

If you are looking for a quick way to generate a pie chart, You can use Panther Classification System for generating such a pie chart. You can either visualize it in a complete/partial ontology level or use your custom gene lists for generating one.

alt text

If you need detailed plot using your own data: you can use a generic GO term enrichment tool and then use the ratio of genes - terms to generate a pie-chart using a standard plotting program/tool.

ADD COMMENTlink written 6.8 years ago by Khader Shameer17k
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