I have a gene, let's say p300, and I have a list of genes that are co-expressed with it. I want to find which of these genes have the most similar function to p300. What would be the best tool for doing this, preferably in R? I was looking at the packages RDavidWebService and FGNet, but maybe someone has a better idea.
Also, my starting list has about 6000 genes, and I want to get roughly the 10 functionally closest genes, so hopefully whatever you all recommend has a way of ranking the functional similarity.
The definition of function is quite ambiguous .
One way is to test semantic similarity, such as GOSemSim based on GO terms. You can have each pair examined and give you a rank/score.
Another is to use curated pathway information, such as gene set/kegg pathway enrichment. You can view which genes are in the same pathway and rank the enrichment of pathway by pvalue. But you don't get a rank for genes. Package clusterProfiler can do this.
Performing functional annotation or gene enrichment analysis including gene annotation and pathway analysis terms using DAVID or some other functional annotation tools available could be useful in this case.
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