Entering edit mode
9.2 years ago
friasoler
▴
50
Hello .-) is someone here familiar with Cytoscape and the apps bingo and cluego?
I'd like to build a good network with the list of genes. Thanks in advance
Roberto
It is a bit vague as question. More details you provide more precise will be the help you are going to get.
Yes you are right. The point is I cant build the network the app ClueGO say there is no terms associated with the list I'm given. Actually the list came from an heterogeneous annotation means gene names from different organisms:
I tried also with out the organism name and using just the names annotated from the same organism. Then if you have any suggestions for me I'll appreciate!
This an example list I'm using:
ClueGO uses GO term, I think the problem is that you organism (or mix of them) is not in their DB. I guess this are orthologous protein among the organisms. If this is the case You can fix this selecting one among Human, Mouse etc. On the other hand you could us a Bioconductor package where you can provide your gen set and you background set, both previously annotated with GO. I really like GOstats and topGO
It would be nice if you add such a long list as external link..;)
Oh thanks for your answer. I'm not familiar with R. I'm just starting in this stuff I know Bioconductor and its power but that a limitation I have right now. Thanks anyway