Online tool for turning Gene Ontology results into figures?

Question

[andre.arrudalima]

Is there any online and free tool that transforms GO output in figures?

Thank you

[Pierre Lindenbaum]

what is a "GO output" ?

[andre.arrudalima]

Gene Ontology output. What we get from Gene Ontology analysis.

[Pierre Lindenbaum]

so , what does it look like ? (for me a GO file is "just" an OBO file or a RDF/XML file)

[andre.arrudalima]

oh, sorry there is a .txt that have enough information for making the figure. then there are .json and .xml options.

The txt looks like this:

Analysis Type:  PANTHER Overrepresentation Test (Released 20221013)
Annotation Version and Release Date:    GO Ontology database DOI:  10.5281/zenodo.6799722 Released 2022-07-01
Analyzed List:  upload_1 (Arabidopsis thaliana)
Reference List: Arabidopsis thaliana (all genes in database)
Test Type:  FISHER
Correction: FDR
GO biological process complete  Arabidopsis thaliana - REFLIST (27430)  upload_1 (20)   upload_1 (expected) upload_1 (over/under)   upload_1 (fold Enrichment)  upload_1 (raw P-value)  upload_1 (FDR)
root morphogenesis (GO:0010015) 670 7   .49 +   14.33   3.15E-07    6.19E-04
plant organ morphogenesis (GO:1905392)  901 7   .66 +   10.66   2.25E-06    3.31E-03
root development (GO:0048364)   1190    9   .87 +   10.37   6.10E-08    3.59E-04
root system development (GO:0022622)    1193    9   .87 +   10.35   6.23E-08    1.83E-04
plant organ development (GO:0099402)    1972    9   1.44    +   6.26    4.21E-06    4.96E-03

Answer 1

[Istvan Albert]

turning into figures

Feels like an overly broad request: what should be on that figure?

If all you wanted is to visualize a gene ontology term you could use a tool like goatools

• https://github.com/tanghaibao/goatools

[andre.arrudalima]

Thank you It was a overly broad request but I specified that needs an online tool. Do you know any?

Answer 2

[geneontologyhelp]

If you just need to grab an image for reference, the PANTHER results display in a table, complete with tabbing that follows the GO hierarchy:

PANTHER (http://www.pantherdb.org/) is the tool that is behind the EA on GO's homepage, in case that is where you were running your analysis from. If you're using the PANTHER site instead of the widget embedded on the GO homepage, you can also select "Functional classification viewed in graphic charts" and then bar chart or pie chart. See also V.D on the PANTHER help page: http://www.pantherdb.org/help/PANTHERhelp.jsp

[andre.arrudalima]

Thank you!

Answer 3

[matthew.pace]

I suggest goatools, but a simple heatmap of the terms may also an option.

Answer 4

[Leite]

Dear @andre.arrudalima

Você pode tentar isso aqui:

Dotplot for filtered pathways result

Abraços Giuseppe