Cytoscape and BINGO app empty output

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4.3 years ago

luzglongoria ▴ 50

Hi,

It is the first time I use cytoscape and I am trying to do some Gene ontology (GO) analyses by using BINGO.

I do all the steps as tutorials say. My select organism is Plasmodium falciparum and I choose the "Paste genes from text" option. Previously I have done some analyses based on RNA-seq that gave me some upregulated genes. By using http://geneontology.org/ I have been able to loo for the gene name/symbol for each gen and included it in cystoscape. The problem is that when I start BINGO the software create a file but is it empty, no error message appears and I don't know what I am doing wrong.

Any help is more than welcome.

Best,

Luz

cytoscape BINGO Gene Ontology RNA-Seq • 1.7k views

ADD COMMENT • link 4.3 years ago by luzglongoria ▴ 50

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Why are you using gene names, are you sure bingo support gene names for your organism of interest?

ADD REPLY • link 4.3 years ago by ashish ▴ 680

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I am using the EnsemblGenome name. Like for instance PF14_0329 for Mitochondrial acidic protein MAM33, putative. Is It that ok ?

ADD REPLY • link 4.3 years ago by luzglongoria ▴ 50

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The gene id for Mitochondrial acidic protein MAM33 is PF3D7_1434800 on ensembl protists. I did not get any results for PF14_0329 on ensembl protists. I think you need to get your ids in the right format. Besides I have never used BINGO, I use clueGO for this purpose, it also supports P. falciparum