CAGE Cluster update

This page is to update information about CAGE clusters on UPDATE_012

CAGE clusters for the main paper

Please contact to fantom5-wp4@gsc.riken.jp about the whole status, and corresponding providers for individual questions.

Expression table with annotation

https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/110804-dpi-clusters-expression

Genomic coordinates

https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/110720-dpi-clusters/

ZENBU configuration

human and mouse

TSS classifier

[Sebastian et al.]

• https://fantom5-collaboration.gsc.riken.jp/webdav/home/seb/update12/documentation_ud12.pdf
• https://fantom5-collaboration.gsc.riken.jp/webdav/home/seb/update12/rescue/documentation_ud12_update.pdf

[Timo]

• https://fantom5-collaboration.gsc.riken.jp/webdav/home/Lassmann/TSS_classification/

Cluster annotations discussed in the cluster working group

Method Description

Transcript model derived annotation protocol

Annotation Results

• webdav repository

Human Decomposition-based Peak Identification (DPI) cluster

• https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/CAGE-Tag-Cluster-Annotation_Aug11/tc.decompose_smoothing_merged.hg19.annotations/
  • tc.decompose_smoothing_merged.hg19.CpGislands.annotated.osc.gz
  • tc.decompose_smoothing_merged.hg19.EST.annotated.osc.gz
  • tc.decompose_smoothing_merged.hg19.Ensembl.non_coding.annotated.sym.osc.gz
  • tc.decompose_smoothing_merged.hg19.Ensembl.protein_coding.annotated.sym.osc.gz
  • tc.decompose_smoothing_merged.hg19.F5_human_lncRNAome.annotated.osc.gz
  • tc.decompose_smoothing_merged.hg19.RefSeq.non_coding.annotated.sym.osc.gz
  • tc.decompose_smoothing_merged.hg19.RefSeq.protein_coding.annotated.sym.osc.gz
  • tc.decompose_smoothing_merged.hg19.TBP_JASPAR_CORE_MA0108.2.annotated.osc.gz
  • tc.decompose_smoothing_merged.hg19.gencode-pseudo.annotated.sym.osc.gz
  • tc.decompose_smoothing_merged.hg19.gencode.non_coding.annotated.sym.osc.gz
  • tc.decompose_smoothing_merged.hg19.gencode.protein_coding.annotated.sym.osc.gz
  • tc.decompose_smoothing_merged.hg19.knownGene.non_coding.annotated.sym.osc.gz
  • tc.decompose_smoothing_merged.hg19.knownGene.protein_coding.annotated.sym.osc.gz
  • tc.decompose_smoothing_merged.hg19.mRNA.annotated.osc.gz
  • tc.decompose_smoothing_merged.hg19.rmsk.annotated.repClass.repFamily.osc.gz

Mouse Decomposition-based Peak Identification (DPI) cluster

• https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/CAGE-Tag-Cluster-Annotation_Aug11/tc.decompose_smoothing_merged.mm9.annotations/
  • tc.decompose_smoothing_merged.mm9.CpGislands.annotated.osc.gz
  • tc.decompose_smoothing_merged.mm9.EST.annotated.osc.gz
  • tc.decompose_smoothing_merged.mm9.Ensembl.non_coding.annotated.sym.osc.gz
  • tc.decompose_smoothing_merged.mm9.Ensembl.protein_coding.annotated.sym.osc.gz
  • tc.decompose_smoothing_merged.mm9.RefSeq.non_coding.annotated.sym.osc.gz
  • tc.decompose_smoothing_merged.mm9.RefSeq.protein_coding.annotated.sym.osc.gz
  • tc.decompose_smoothing_merged.mm9.TBP_JASPAR_CORE_MA0108.2.annotated.osc.gz
  • tc.decompose_smoothing_merged.mm9.knownGene.non_coding.annotated.sym.osc.gz
  • tc.decompose_smoothing_merged.mm9.knownGene.protein_coding.annotated.sym.osc.gz
  • tc.decompose_smoothing_merged.mm9.mRNA.annotated.osc.gz
  • tc.decompose_smoothing_merged.mm9.rmsk.annotated.repClass.repFamily.osc.gz

Other clusters on UPDATE_012

Please don't hesitate to use/produce other clusters for other purposes

• by Maritn Frith https://fantom5-collaboration.gsc.riken.jp/webdav/home/mcfrith/110725-update012-pclu/
• by Michael Rehli https://fantom5-collaboration.gsc.riken.jp/wfebdav/home/rehli/
• by Cesare Furlanello, Marco Chierici, Davide Albanese, Marco Roncador - https://fantom5-collaboration.gsc.riken.jp/webdav/home/FBK/110905-clusters/

Related pages

• Clustering evaluation - see here for the clustering 'competition', which is performed on UPDATE_011
• Promoter definition