interactions: Dataset containging interactions of the Kinase-Phosphatase...

In VertexSort: Network Hierarchical Structure and Randomization

Description

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).

Usage

data("interactions")

Format

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

Details

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.

Source

Abd-Rabbo, D. and Michnick, S.W. 2017 BMC Syst Biol 11.

References

Sharifpoor, S., Nguyen, Ba. A.N., Young, J.Y. et al. 2011 Genome Biol 12, R39.

Examples

  ## 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

VertexSort documentation built on May 2, 2019, 9:12 a.m.