dna: Dna damage data set (PPI and expression)

In netresponse: Functional Network Analysis

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)

Example output

Loading required package: Rgraphviz
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: grid
Loading required package: minet
Loading required package: mclust
Package 'mclust' version 5.4.7
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: reshape2

netresponse (C) 2008-2020 Leo Lahti et al.

https://github.com/antagomir/netresponse

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