How to perform GO enrichment using BiNGO at Cytoscape

Question

[Kumar]

Hi,

I am looking to perform GO enrichment analysis using BiNGO Cytoscape. I have generated a csv file includes columns such as NCBI ID and Gene Ontology ID. I am trying to run BiNGO but it shows following message (attached image). Please advise which type of format does BinGO require to perform GO enrichment.

Input csv file format:

XP_024449205.1  GO:0008152
XP_024449205.1    GO:0003824
XP_006841530.1  GO:0050896
XP_018839917.1  GO:0008152

Answer 1

[boczniak767]

You should use gene association file outlined at GO website "Types of GO annotation files" section. It boils down to adding few required columns.

Maybe there is somewhere such file for your organism? I'd advise to look for it.

[Kumar]

Thank you for the information. However, I am uncertain if I am able to arrange all the required fields as per the GAF format. I have the following type of data in my file.

XP_006845785.1  GO:0008152-metabolic_process(L=1),GO:0009987-cellular_process(L=1), GO:0005576-extracellular_region(L=1),   GO:0003824-catalytic_activity(L=1),GO:0005488-binding(L=1),
XP_025797078.1  GO:0008152-metabolic_process(L=1),GO:0009987-cellular_process(L=1),GO:0044699-single-organism_process(L=1),GO:0071840-cellular_component_organization_or_biogenesis(L=1),   GO:0005623-cell(L=1),GO:0016020-membrane(L=1),  GO:0005488-binding(L=1),
XP_019108059.1  GO:0008152-metabolic_process(L=1),GO:0009987-cellular_process(L=1),GO:0044699-single-organism_process(L=1),GO:0051179-localization(L=1),    GO:0005623-cell(L=1),GO:0016020-membrane(L=1),GO:0043226-organelle(L=1),    GO:0003824-catalytic_activity(L=1),GO:0005215-transporter_activity(L=1),GO:0005488-binding(L=1),
XP_027940045.1  GO:0008152-metabolic_process(L=1),GO:0009987-cellular_process(L=1), GO:0005623-cell(L=1),GO:0016020-membrane(L=1),GO:0043226-organelle(L=1),    GO:0003824-catalytic_activity(L=1),GO:0005488-binding(L=1),
XP_021830538.1  GO:0008152-metabolic_process(L=1),GO:0009987-cellular_process(L=1),GO:0044699-single-organism_process(L=1),GO:0065007-biological_regulation(L=1),   GO:0005623-cell(L=1),GO:0016020-membrane(L=1),GO:0032991-macromolecular_complex(L=1),GO:0043226-organelle(L=1), GO:0003824-catalytic_activity(L=1),

[boczniak767]

The starting point is gene - GO association. So you can make a file like this (an example for the first gene):

XP_006845785.1 GO:0008152
XP_006845785.1 GO:0009987
XP_006845785.1 GO:0005576
XP_006845785.1 GO:0003824
XP_006845785.1 GO:0005488

As a second step, you can use file with GO id and GO name and join it with above file. Unfortunately, I don't remember, from where I downloaded abovementioned file - it should be somewhere at the GO website. Edit: You can also retrieve GO names using biomart or of course use names from your file.

[Kumar]

Thank you for your suggestion. I tried providing the input files like these following ways but once I select the organism (e.g. Arabidopsis) in BiNGO setting, it shows the message "May chose the wrong type of gene identifier". If I ran it without selecting any model organisms, it runs continuously for long time..

XP_006845785.1=0008152
XP_006845785.1=0009987
XP_006845785.1=0005576
XP_006845785.1=0003824
XP_006845785.1=0005488

Input file use GO terms and names:

GO:0005488=binding
GO:0005215=transporter_activity 
GO:0043226=organelle

[boczniak767]

I'm sorry, I was not precise. The file structure that I proposed is just a first step to make a gene association file, which must follow specifications listed on GO website. Maybe download gaf file for one of the organisms and look at it in a spreadsheet, it will give you information about structure. It is worth noting, that some columns can be left empty, and some other will accept any text.

[Kumar]

Hi, I downloaded a GO annotation file of Arabidopsis from (http://current.geneontology.org/products/pages/downloads.html) and provided at BiNGO in select "annotation section". However, it still shows the message "None of the label in annotation match with the chosen ontology, please check their compatibility". To verify I just used some GO terms from the annotation file but still it shows the same error. Do you have any idea. Thank you!!

[boczniak767]

As I can see from your screenshot you work with yeast, so it won't work with gaf file for other organism. In other words, both gaf file and your network must have identifiers (of the same type) for the same organism. However, for the sake of tests you can change Arabidopsis ids to your yeast ids. This will give you information, if Go analysis works.

[Kumar]

My data is not from yeast. I have a tree species that is not in the list of BiNGO so I downloaded the gaf annotation file of Arabidopsis and selected as custom in BiNGO. In the screenshot I was just trying with selecting a reference species from the list.

[Kumar]

How I get result from BiNGO if my working species is not in the list. It is giant sequoia tree.