I want to construct a Gene Ontology Network from my gene list. The problem is that these genes don’t belong to a same organism (they belong to different prokaryotic species) and some of these genes are repetitive. My objective is to retrieve some common functional and molecular attributes for this set of genes.
I tried a number of Cytoscape apps, such as BINGO and ClueGO, but I can’t build any network. I think that the main reason was that my genes don’t belong to a same organism.
Does anyone know a solution (like an appropriate software) for this problem? Thanks
My guess is that you have genes that do not have annotations. I would check a functional annotation site (something like David http://david.abcc.ncifcrf.gov) before doing anything else, though be careful since these sites may not have complete coverage of prokaryotic genes. If you have sequence, maybe look at Blast2GO.
Most of these genes were retrieved from Swiss-Prot and they are manually annotated. The problem is that these annotations are separated. I want to put together these annotation in a network in order to find some common parts. Thank you for your time and consideration.
What I understand is that you have GO annotations in separate text files of the same format. In that case, then you just need to merge them together in order to be able to use them with most tools. This is straightforward from the command line -- just search for something like "merge files command line" with whatever computer you are using.
Personally, if I were looking for common features within a set of genes, I would go with a Formal Concept Analysis tool (conexp is one). The construction would give you biclusters (called formal concepts) between genes and annotations. It requires a little more understanding, because biclusters relate in more complicated ways. However, it shows you subtleties that the concept network does not. Having redundant homologues could make things more messy, but as long as they mostly have the same annotations they will end up in the same biclusters.
salam
fekr mikonam behtarin kar baraye kare shoma blast kardan gene ha dar goone haye mokhtalef va sakhtane yek genome reference hast,be in soorat k az gooneye morede nazaretoon oon tedad gene ke vojood dare ro barmidarid va baghiye gene ha ro az tarighe peyda kardane oon gene ha dar goone haye dige va blast kardaneshoon va peyda kardane olgoo haye polymorphismi sahabihsazi mikonin, ba in ravesh gene haye gooneye morede nazaretoon ro bazsazi kardin va az hamin gene ha baraye motaleate ontology dar in goone estefade mikonid
I found a solution ! This Tutorial (Gene Ontology Enrichment Network Analysis) was really helpful to me.
http://www.slideshare.net/dgrapov/proteomics-workshop-2014-lab-dmitry-grapov
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