RedeR (version 1.20.0)

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

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 ('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)