osmo: Osmoshock data set (PPI and expression)

In netresponse: Functional Network Analysis

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.

Examples

data(osmo)

netresponse documentation built on Nov. 8, 2020, 5:04 p.m.