Dataset Open Access

Transcription initiation peaks based on FANTOM5 CAGE data on hg38 and mm10

Kawaji, Hideya

Overview

Decomposition-based peak identification (DPI, https://github.com/hkawaji/dpi1) is applied to the re-processed (re-aligned) FANTOM5 data, upon hg38 (GRCh38) and mm10 (GRCm38), obtained from below:

  • http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v1/basic/
  • http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v1/basic/

The same parameters to the ones used in the previous paper (Forrest ARR, Kawaji H, Rehli M, et al. Nature 507: 462–470, 2014) was used.

 

Data files

Four data files per assembly are prepared as below.

  1. tag cluster in the original definition (*.tc.bed.gz)
  2. full set of DPI peaks (*.tc.decompose_smoothing_merged.bed.gz)
  3. permissive set of DPI peaks (*.tc.decompose_smoothing_merged.ctssMaxCounts3.bed.gz)
  4. robust set of DPI peaks (*.tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.bed.gz)

 

Acknowledgement

This data set is supported by Research Grant from MEXT to RIKEN Preventive Medicine and Diagnosis Innovation Program, RIKEN Center for Life Science Technologies, and JSPS KAKENHI Grant-in-Aid for Scientific Research No. 16H02902.

Files (285.8 MB)
Name Size
hg38.tc.bed.gz
md5:e4a92ee2a4e46799b064007e0b8efa8c
50.8 MB Download
hg38.tc.decompose_smoothing_merged.bed.gz
md5:53486de3eefd37b4c334cca5bb9183cc
76.8 MB Download
hg38.tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.bed.gz
md5:2a0f2f9e1f20b57825bf9a6e9c1cf119
4.3 MB Download
hg38.tc.decompose_smoothing_merged.ctssMaxCounts3.bed.gz
md5:54e06e2b695f8099d2cf2b040a23c967
24.4 MB Download
mm10.tc.bed.gz
md5:9452026af409536eb522d9f99cf861db
41.6 MB Download
mm10.tc.decompose_smoothing_merged.bed.gz
md5:13e8bf2f79e0dda809996cab6239b077
63.2 MB Download
mm10.tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.bed.gz
md5:769a7bb440988b271258807dc0677e6a
3.4 MB Download
mm10.tc.decompose_smoothing_merged.ctssMaxCounts3.bed.gz
md5:c714c6270bd09430cdf02d754df32035
21.3 MB Download
  • Decomposition-based peak identification (DPI), https://github.com/hkawaji/dpi1
  • Forrest ARR, Kawaji H, Rehli M, et al. Nature 507: 462–470, 2014
  • Lizio M, Harshbarger J, Abugessaisa I, Nucleic Acids Res 45: D737–D743, 2017
  • Lizio M, Harshbarger J, Shimoji H, et al. Genome Biol 16: 22, 2015

Share

Cite as