ppiPre (version 1.9)

TCSSGeneSim: Topological Clustering Semantic Similarity(TCSS) Between two Genes

Description

Given two genes, this function will calculate the TCSS between them

Usage

TCSSGeneSim(gene1, gene2, ont = "MF", organism = "yeast", drop = "IEA")

Arguments

gene1
Entrez gene id.
gene2
Another entrez gene id.
ont
One of "MF", "BP", and "CC" subontologies.
organism
One of "anopheles", "arabidopsis", "bovine", "canine", "chicken", "chimp", "ecolik12", "ecsakai", "fly", "human", "malaria", "mouse", "pig", "rat", "rhesus", "worm", "xenopus", "yeast" and "zebrafish."
drop
A set of evidence codes based on which certain annotations are dropped. Use NULL to keep all GO annotations.

Value

geneSim
Semantic similarity.
GO1
Corresponding GO terms for gene1.
GO2
Corresponding GO terms for gene2.

References

[1] S. Jain and G. Bader, "An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology", BMC Bioinformatics, vol. 11, no. 1, p. 562, 2010.

[2] G. Yu, F. Li, Y. Qin, X. Bo, Y. Wu, and S. Wang, "GOSemSim: an R package for measuring semantic similarity among GO terms and gene products", Bioinformatics, vol. 26, no. 7, pp. 976-978, Apr. 2010.

See Also

IntelliGOGeneSim

Examples

Run this code
  #TCSSGeneSim("1134", "1145", ont="MF", organism="human")
  #TCSSGeneSim("YOR065W", "YEL024W", ont="CC", organism="yeast", drop="IEA")

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