ppi.CC: Yeast protein interaction network

In sand: Statistical Analysis of Network Data with R, 2nd Edition

Description

A network of 241 interactions among 134 proteins. They were assembled by Jiang et al. (see below), from various sources, and pertain to only those proteins annotated, as of January 2007, with the term “cell communication” in the gene ontology (GO) database.

Usage

ppi.CC

Format

An undirected igraph graph object, with vertex attributes:

• ‘name’: the name of the protein.

• ‘ICSC’: whether the protein is annotated with the “intracellular signaling cascade” GO term, zero or one.

• ‘IPR000198’: whether the protein contains the ‘rho GTPase-activating protein domain’ (IPR000198) motif.

• ‘IPR000403’: whether the protein contains the ‘phosphatidylinositol 3-/4-kinase, catalytic domain’ (IPR000403) motif.

• ‘IPR001806’: whether the protein contains the ‘small GTPase superfamily’ (IPR001806) motif.

• ‘IPR001849’: whether the protein contains the ‘pleckstrin homology domain’ (IPR001849) motif.

• ‘IPR002041’: whether the protein contains the ‘ran GTPase’ (IPR002041) motif.

• ‘IPR003527’: whether the protein contains the ‘mitogen-activated protein (MAP) kinase, conserved site’ (IPR003527) motif.

Source

See the reference below. Please cite it if you use this dataset in your work.

References

X. Jiang, N. Nariai, M. Steffen, S. Kasif, E. Kolaczyk: Integration of relational and hierarchical network information for protein function prediction. BMC Bioinform. 9, 350 (2008).

sand documentation built on July 8, 2020, 7:16 p.m.