Description Usage Format Details Source References Examples
Vector of Oct4 bound genes predicted by analyzing ESC ChIP-seq data from GSE11724.
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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
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.
www.ncbi.nlm.nih.gov/geo/
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.
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