Software for Gene ontology enrichment graph

Question

[yepeh72919]

I have the following gene enrichment from a ChIP-seq experiment. The highest p-values are not from the GO database, but from other databases like COSMIC, BIOCYC, MSigDB etc.

Is there any software similar to AmiGO and QuickGO that I can use to visualize the directed acyclic graphs (DAG)?

Is it even possible to create DAG with enrichment from different databases? Would be super grateful if someone could point me in the right direction!

Thanks so much!

Here is an example of my results:

Database | TermID

COSMIC | angiosarcoma

COSMIC | blood_vessel

COSMIC | soft tissue_haemangioma

MSigDB | DACOSTA_UV_RESPONSE_VIA_ERCC3_DN

[lessismore]

http://bioinfo.cau.edu.cn/agriGO/analysis.php
here you can choose a customized annotation + customized reference.

[yepeh72919]

thanks! I checked it just now (2020 Jan 23 9:50 AM PST) and it seems like the site was down

Answer 1

[svp]

Webgestalt ClueGO

[yepeh72919]

I am not sure if Webgestalt can allow me to use a customised annotation. My parameters are: Method of Interest: Gene Set Enrichment Analysis (GSEA) Functional Database: geneontology; biological process

Then I uploaded my peaks and the max height of my peaks to run the analysis. Please let me know if I am doing something wrong or missing the features of Webgestalt.

[svp]

ClueGO is a cytoscape plugin where you can select customised annotation and there are lots of other parameters to play with.

Also did you try ToppGene Suit

[yepeh72919]

Thanks a lot! My aim is to find some interesting genes from the gene ontologies. I was trying clueGO and it seems like there is a function for custom reference set, which may potentially be helpful for what I am looking for. Actually, I am interested in endothelial cell proliferation gene ontologies, so I was wondering if I could use endothelial cell proliferation (GO:0001935) as a reference list in order to obtain ontologies that are somewhat related to proliferation. My gene ontologies using GO:biological processes are related to neurons. I tried doing that but there was a pop-up that there are no GO terms/pathways found. (i already used 1#/% of genes/terms), so I'm not sure if I'm cherrypicking my data by using the custom reference set and affecting this analysis.

I will try ToppGene Suit and let you know! Once again, I really appreciate your time!