osmo: Osmoshock data set (PPI and expression)
In antagomir/netresponse: Functional Network Analysis

osmo	R Documentation

Osmoshock data set (PPI and expression)

Description

A combined yeast data set with protein-protein interactions and gene expression (osmotick shock response). 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: 1711, number of interactions: 10250, number of gene expression observations: 133, number of total links with PPI and expression links: 14256.

Usage

data(osmo)

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.

O'Rourke, S. and Herskowitz, I. Unique and redundant roles for Hog MAPK pathway components as revealed by whole-genome expression analysis. Molecular Biology of the Cell 2004, 15:532-42.