2014-07-11
Marina Lizio (marina.lizio@riken.jp)
Inquiries to fantom-help@gsc.riken.jp

Description of the columns in CAGE peaks coordinates files:
chromosome
start of CAGE peak region
end of CAGE peak region
name (ID) of the CAGE peak
cumulative score across all samples
strand of the CAGE peak
start of the representative TSS position
end of the representative TSS position (Note: end is always start+1)
rgb string for color coding (plus or minus strand only)

2014-02-05
Coordinate bed files for both human and mouse CAGE peaks were added. Both robust set and permissive set of peaks are available.
hg19.cage_peak_coord_*.bed.gz
mm9.cage_peak_coord_*.bed.gz
 
2012-12-07
Marina Lizio (marina.lizio@riken.jp)
Clustering of CAGE TSS following DPI method (kawaji@gsc.riken.jp)
This folder contains CAGE peaks expression tables for the robust set of peaks. Annotations are provided for the permissive set of peaks.

hg19.cage_peak_ann.txt.gz - CAGE peak based table with annotated peaks for human samples
hg19.cage_peak_tpm.osc.txt.gz - CAGE peak based expression table (RLE normalized) for human samples [see edgeR documentation for further details about normalization method]
hg19.cage_peak_counts.osc.txt.gz - CAGE peak based expression table for human samples
hg19.cage_peak_tpm_ann.osc.txt.gz - CAGE peak based expression table (RLE normalized) for human with annotation
hg19.cage_peak_counts_ann.osc.txt.gz - CAGE peak based expression table for human with annotation
hg19.cage_peak_relative_expr.txt.gz - CAGE peak based relative expression (log10 expression relative to median) for human
mm9.cage_peak_ann.txt.gz - CAGE peak based table with annotated peaks for mouse samples
mm9.cage_peak_tpm.osc.txt.gz - CAGE peak based expression table (RLE normalized) for mouse samples
mm9.cage_peak_counts.osc.txt.gz - CAGE peak based expression table for human samples
mm9.cage_peak_tpm_ann.osc.txt.gz - CAGE peak based expression table (RLE normalized) for mouse with annotation
mm9.cage_peak_counts_ann.osc.txt.gz - CAGE peak based expression table for mouse with annotation
mm9.cage_peak_relative_expr.txt.gz - CAGE peak based relative expression (log10 expression relative to median) for mouse