This dataset contains a data frame called interactions containing the binary interactions assembled in the kinase-phosphatase network. Interactions were obtained from the Kinase Interaction Database (Sharifpoor et al.) and from other data curation efforts (Abd-Rabbo et al. 2017).
This data frame contains 1087 rows and the following columns:
standard name (ORF) of the kinase/phosphatase that phosphorylates/dephosphorylates the substrate
standard name (ORF) of the protein substrate phosphorylated/dephosphorylated by the kinase/phosphatase
These interactions represent binary interactions between kinases/phosphatases and their substrates. They were used in (Abd-Rabbo et al. 2017) to form the kinase-phosphatase network used with the Vertex Sort algorithm to study the hierarchical structure of the signaling regulatory network in the budding yeast.
Abd-Rabbo, D. and Michnick, S.W. 2017 BMC Syst Biol 11.
Sharifpoor, S., Nguyen, Ba. A.N., Young, J.Y. et al. 2011 Genome Biol 12, R39.
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## load the VertexSort library library(VertexSort) ## load interactions of the kinase-phosphatase network (kp-net) data(interactions) ## view the dimentions of the interactions data frame dim(interactions) ## view the top of the interactions data frame head(interactions) ## The interactions data frame could be loaded into an R session ## and used as an example to apply on it the vertex sort algorithm ## or generate radom networks. See ?vertex.sort, ?dpr, ?sdpr, ?dnpr, ## ?idpr and ?odpr
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