Question: How to calculate GOsimilarity between different species
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gravatar for teresa.noviello89
3.1 years ago by
Italy
teresa.noviello890 wrote:

Hi; I'd like to know if it is possible to calculate similarities between GO terms or genes from two different species. I know that some Bioconductor packages like GOSemSim or GOSim compute this, but it is olway intraspecie. Is it possible to do this kind of analysis inter-species? Thanks

ADD COMMENTlink modified 2.7 years ago by e.rempel790 • written 3.1 years ago by teresa.noviello890
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gravatar for Jean-Karim Heriche
3.1 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche21k wrote:

You can compute semantic similarities between terms and genes across species because you can consider annotations of genes in both species as one corpus and use this to compute the frequency of each term which is the basis for all information content-based similarity measures. Most R packages have pre-computed species-specific terms similarities to be fast. For custom use, I would suggest the dnet R package. You could do something like (untested):

ig.GOBP <- dRDataLoader(RData='ig.GOBP') # GO biological process domain
gene_annotations <- read.csv("gene_annotations.txt", header=F, sep="\t")
dag <- dDAGannotate(ig.GOBP, annotations=gene_annotations, path.mode="all_paths")
sim <- dDAGgeneSim(g=dag, genes=gene_list, method.gene="max", method.term="Resnik")
ADD COMMENTlink written 3.1 years ago by Jean-Karim Heriche21k
0
gravatar for e.rempel
2.7 years ago by
e.rempel790
Germany, Heidelberg, COS
e.rempel790 wrote:

Hi,

you could actually use GOSemSim package to calculate semantic similarity of two groups of GO terms, whereby the groups could be from different species. For this purpose, you could use the function mgoSim

ADD COMMENTlink written 2.7 years ago by e.rempel790
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