RedeR.data {RedeR} | R Documentation

## 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 <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)

[Package RedeR version 1.35.0 Index]