Cytoscape GO Enrichment Annotation file trouble (BiNGO)
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8 months ago

Hi everyone and thank you in advance.

I Have a list of genes that i got from a module from WCGNA coex network. Those are the first lines of my list

EGR_11308
EGR_11303
EGR_11301
EGR_11292
EGR_11271
EGR_11270
EGR_11255
EGR_11254
EGR_11197
EGR_11194

There are about 1.500 genes. THe organism is Echinococcus granulosus. So i got the annotation files from here:

https://www.ncbi.nlm.nih.gov/genome/?term=echinococcus+granulosus

The format files that i downloaded are: gff.gz , gbbf.gz and .csv Reading some information, im understandig that to use BiNGO , my annotation file must be .obo and i could find that file HERE , but the organism wich im working (Echinococcus granulosus), is not there...

Is there any way to convert the gz files to .obo files??? Im a little bit confused, not really sure if im not understanding something....

thank you everyone!

RNA-Seq cytoscape go analysis • 408 views
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Entering edit mode
8 months ago
scooter ▴ 450

Greetings,

In order to use BiNGO for a non-model species, you actually need two files -- an annotation file, which indicates which terms each gene has, and an ontology file, which represents a hierarchy of terms. You can't convert an annotation file into an ontology file since it doesn't contain the hierarchical information. There are a couple of approaches you can take. First, I would see if your species is available in ClueGO, which is another Cytoscape app often used for enrichment. If that doesn't work, you can check and see if your species is in STRING (actually, I checked, and it's not, but Echinococcus multilocularis is) and if it is, you can use the stringApp to convert your network to a STRING network and perform enrichment. Finally, you could use g:Profiler manually for each group of genes. There is a new Cytoscape app called CyCommunityDetection that combines community detection (clustering) with enrichment, but I don't know how well that would work if your data set is already clustered.

-- scooter

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Hi Scooter and sorry for my late answer. I have seen STRING and ClueGO and there is no E granulosus information. I have used gProfiler already, for each group of genes.

I was trying to use BiNGO cause some guys that worked with E granulosus told me that they worked with BiNGO... but i do not know how they do...is not enough having the ontology file and the annotation file that i got from here https://www.ncbi.nlm.nih.gov/genome/?term=echinococcus%20granulosus ?

THank you again!

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