Cytoscap-BINGO App for zebrafish data

Question

[rajasekargutha]

i am working with Zebrafish genomic data, and i want to make DAG graph for gene ontology terms using BINGO in Cytoscape. But its not showing zebrafish under organisms type.

[EVR]

Did you check the version of app.? If it is the latest version and still you didn’t have organism listed, there is a tutorial provided to find GO enrichment for non-model organism. Kindly refer to it. If you still have problems, do let me know, I will guide you

[rajasekargutha]

Could you send the tutorial link

[rajasekargutha]

i am dowloaded gene annotation file from geneontology.org, how to proceed further......

[EVR]

http://www.psb.ugent.be/cbd/papers/BiNGO/Customize.html

[rajasekargutha]

i have gone through that link and downloaded files from geneontology org site. i uploaded files under custom panel in bingo, and i clicked on start bingo but i got error that Data File: FILE NAMING ERROR: java.lang.NullpointerException

[rajasekargutha]

Could you guide me please

Answer 1

[Chirag Parsania]

Hi,

Download gene association file (not annotation file) for any organism from geneontology database. Then use "custom" under organism selection in bingo and select file you downloaded. Here is the link for zebrafish.

Hope this works.

Chirag.

[rajasekargutha]

what is .obo file and how to use this and where i can correct .obo file for zebrafish

Answer 2

[Chirag Parsania]

The link I shared will download "gene_association.zfin" file. Where did you get .obo file ? Is it output of bingo ? Give more details.