dna {netresponse} | 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.

### Examples

    data(dna)

[Package netresponse version 1.50.0 Index]