Oct4ESC_ChIPgenes: Predicted Oct4 bound genes in embryonic stem cells (ESC)...

In ChIPXpress: ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles

Description

Vector of Oct4 bound genes predicted by analyzing ESC ChIP-seq data from GSE11724.

Usage

data(Oct4ESC_ChIPgenes)

Format

A data frame with 5158 observations on the following 21 variables.

Rank

a numeric vector

Chr

a character vector

Start

a numeric vector

End

a numeric vector

Strand

a character vector

Annotation

a character vector

Gene

a character vector

EntrezID

a numeric vector

peak_length

a numeric vector

FDR

a numeric vector

left_peakboundary

a numeric vector

right_peakboundary

a numeric vector

peak_summit

a numeric vector

bound_center

a numeric vector

bound_width

a numeric vector

maxT

a numeric vector

maxT_pos

a numeric vector

max_log2FC

a numeric vector

maxFC_pos

a numeric vector

minuslog10_minPoisP

a numeric vector

minPoisP_pos

a numeric vector

Details

To obtain the TF bound gene predictions, the ChIP-seq data is processed using CisGenome with the default parameters. Only peaks significant at a FDR of 0.10 are retained and annotated by assigning peaks to genes if the peak falls within 10kbp upstream or 5kbp downstream of the gene transcription start site. Only the highest ranking peak for each gene is retained in the data frame for input. To be clear, the Rank in the data frame corresponds to the original peak ranking by CisGenome. The ChIPx ranking is simply the order of genes in the data frame.

Source

www.ncbi.nlm.nih.gov/geo/

References

Marson A. et al. (2008) Connecting microRNA genes to the core trancsriptional regulatory circuitry of embryonic stem cells. Cell 134, 521-533.

Barrett T., et al. (2007) NCBI GEO: mining tens of millions of expression profiles - database and tools update. Nucl. Acids Res. 35, D760-D765.

Examples

data(Oct4ESC_ChIPgenes)

ChIPXpress documentation built on Nov. 8, 2020, 4:58 p.m.