proteinInteraction: Protein interaction for yeast

In xnet: Two-Step Kernel Ridge Regression for Network Predictions

Description

A dataset for examining the interaction between proteins of yeast. The dataset consists of the following objects:

Usage

proteinInteraction

Format

• proteinInteraction: a numeric square matrix with 150 rows/columns

• Kmat_y2h_sc: a numeric square matrix with 150 rows/columns

Details

• proteinInteraction: the label matrix based on the protein network taken from the KEGG/PATHWAY database

• Kmat_y2h_sc: a kernel matrix indicating similarity of proteins.

The proteins in the dataset are a subset of the 769 proteins used in Yamanishi et al (2004). The kernel matrix used is the combination of 4 kernels: one based on expression data, one on protein interaction data, one on localization data and one on phylogenetic profile. These kernels and their combination are also explained in Yamanishi et al (2004).

Source

https://doi.org/10.1093/bioinformatics/bth910

References

Yamanishi et al, 2004: Protein network inference from multiple genomic data: a supervised approach.

xnet documentation built on Feb. 4, 2020, 9:10 a.m.