BiNGO doesn't work with custom reference file

[Giuseppe Puglia]

Hi,

I'm using BiNGO application to make an enrichment analysis from RNAseq expression analysis data obtained with Cufflinks. These are the settings I used:

- Paste Genes from Text: 

TCONS00000005

TCONS00000006

TCONS00000007

TCONS00000012

TCONS00000057

TCONS00000068

TCONS00000070

TCONS00000082

...

- Select Reference set:

(species=Cynara cardunculus)(type=Biological Process)(curator=GO)

TCONS00000068 = 0009507

TCONS00000068 = 0009523

TCONS00000068 = 0016021

TCONS00000068 = 0045156

TCONS00000068 = 0046872

TCONS00000068 = 0009772

TCONS00000070 = 0009507

...

- Select Ontology file:

the go.obo file, Core ontology (OBO Format), downloaded from the geneontology consortium website.

I checked the box for saving data and when I press "Start BiNGO" the program is stuck on hourglass and a file of 0 byte is created.

Thank you for any help.

Giuseppe

[Piet]

Hi Guiseppe,

Of course the lack of an error message is rather inappropriate but did you select the proper gene annotation file also?

Cheers, 
Piet

Op dinsdag 20 december 2016 12:03:19 UTC+1 schreef Giuseppe Puglia:

[Giuseppe Puglia]

Hi Piet,

thank you for your answer. I both tried selecting Arabidopsis thaliana from the menù and without making any selection ("---" option), but in any case I did not obtained any result. Could be something wrong in my files? May I send you the reference file and the gene list?

Cheers,

Giuseppe

[angelicaca...@gmail.com]

Hi all,

I'm having the same problem: a file of 0 byte is created.
I'm working with virus and followed the tutorial described here (https://www.psb.ugent.be/cbd/papers/BiNGO/Customize.html).

I've found just one difference in this tutorial. For 'select reference set' config, only 'Use whole annotation as reference set' and 'Use network as reference set' are available. 'Test cluster versus whole annotation' is not available any more.

Below I present my simple example.

==
My setup is as follows:
- cytoscape: 3.5.0
- BINGO: 3.0.3

Gene list:
BRLF1
BKRF4
EBNA-3B
BMRF1


My custom annotation file:
(species=Human gammaherpesvirus 4 typo 2)(type=Biological Process)(curator=GO)
BRLF1 = 0006355
BRLF1 = 0032583
BRLF1 = 0045449
BRLF1 = 0061019
BKRF4 = 0019012
BKRF4 = 0019033
EBNA-3B = 0016032
EBNA-3B = 0042025
BMRF1 = 0006355
BMRF1 = 0006351

and I'm using the updated ontology file 'goslim_generic.obo'.