Description Usage Format Details Source References Examples
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).
1 | data("interactions")
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This data frame contains 1087 rows and the following columns:
kp_orf
standard name (ORF) of the kinase/phosphatase that phosphorylates/dephosphorylates the substrate
substrate_orf
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ## 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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