Plotting A Pie-Chart Of Molecular Function Using Gene Ontology Method?

Question

[J.F.Jiang]

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!

[Jeremy Leipzig]

please upload an example of what you are talking about

Answer 1

[Ian]

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

CateGOrizer

REViGO (not a pie chart, but interesting display)

Answer 2

[Caddymob]

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}

[J.F.Jiang]

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?

Answer 3

[Khader Shameer]

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.

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.