RedeR.data: Pre-processed dataset for RedeR case study.

In RedeR: Interactive visualization and manipulation of nested networks

Description

Preprocessed data from a time-course gene expression and ChIP-on-chip analysis of estrogen receptor (ER) binding sites in MCF7 breast cancer cell line (Carroll et al, 2006).

Usage

data(Carroll2006)

Format

Carroll2006 List containing 'exp', 'tgs', 'ids', and 'bdsites' R objects.

Details

The gene expression dataset consists of 12 time-course Affymetrix U133Plus2.0 microarrays: 3 replicates at 0h, 3 replicates at 3h, 3 replicates at 6h and 3 replicates at 12h. The original dataset is available at GEO database (GSE11324). The gene ER binding site dataset consists of a Bed file of ER ChIP-on-chip experiment. The original dataset is available at http://research.dfci.harvard.edu/brownlab/datasets/index.php (ER sites from the Bed file '1E-5.bed').

Carroll2006$exp

data.frame with log2 gene expression dataset.

Carroll2006$tgs

data.frame with microarray details (e.g. targets for limma analysis).

Carroll2006$ids

data.frame with gene ids used in RedeR case study.

Carroll2006$bdsites

data.frame with ER binding sites mapped to genome build GRCh37.

hs.inter

Human interactome extracted from the Human Protein Reference Database (HPRD) in April 2011 <igraph object> ('name' attribute is mapped to ENTREZ ID).

ER.limma

data-frame containing pre-processed results from limma analysis and ER binding sites mapped to differentially expressed (DE) genes. Content: annotation (ENTREZ and Symbol), time-course fold change (logFC.t3, logFC.t6, logFC.t12), p values (p.value.t3, p.value.t6, p.value.t12), DE genes (degenes.t3, degenes.t6, degenes.t12) and distance of the closest ER bd site to the TSS – in kb (ERbdist).

ER.deg$dat

Summary from ER.limma data object with extracted data for differentially expressed genes only.

ER.deg$exp

Data matrix with log2 gene expression values of DE genes.

ER.deg$ceg

Co-expression gene network of early ER-responsive genes computed by the function cea cea.

References

Carroll JS et al., Genome-wide analysis of estrogen receptor binding sites. Nat Genet. 38(11):1289-97, 2006.

Examples

    data(Carroll2006) 
    data(hs.inter)
    data(ER.limma)
    data(ER.deg)

Example output

***This is RedeR 1.24.1! For a quick start, please type 'vignette('RedeR')'.
   Supporting information is available at Genome Biology 13:R29, 2012,
   (doi:10.1186/gb-2012-13-4-r29). 

RedeR documentation built on Nov. 8, 2020, 7:45 p.m.