dna: Dna damage data set (PPI and expression)
In antagomir/netresponse: Functional Network Analysis

dna	R Documentation

Dna damage data set (PPI and expression)

Description

A combined yeast data set with protein-protein interactions and gene expression (dna damage). Gene expression profiles are transformed into links by computing a Pearson correlation for all pairs of genes and treating all correlations above 0.85 as additional links. Number of genes: 1823, number of interactions: 12382, number of gene expression observations: 52, number of total links with PPI and expression links: 15547.

Usage

data(dna)

Format

List of following objects:

ppi: PPI data matrix
exp: gene expression profiles data matrix
gids: Vector of gene ids corresponding to indices used in data matrices
obs: Gene expression observation details
combined.links: pooled matrix of PPI and expression links

Source

PPI data pooled from yeast data sets of [1] and [2]. Dna damage expression set of [3].

References

Ulitsky, I. and Shamir, R. Identification of functional modules using network topology and high-throughput data. BMC Systems Biology 2007, 1:8.

Nariai, N., Kolaczyk, E. D. and Kasif, S. Probabilistic Protein Function Predition from Heterogenous Genome-Wide Data. PLoS ONE 2007, 2(3):e337.

Gasch, A., Huang, M., Metzner, S., Botstein, D. and Elledge, S. Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mex1p. Molecular Biology of the Cell 2001, 12:2987-3003.