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.

'Promotome' set

Note that the set is not finalized yet. The current status is promotome v1.0 RC1, where only the CAGE clusters supported by independent resources (evidences) are included.

• available data: expression and human readable (but computer-generated) description for each clsuter. See method for the cluster description here: 110926-promotome-v1.0-RC1.pdf
• directory: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/110804-dpi-clusters-expression
• 'annotations' discussed by the cluster working group (see below) is not included yet - rough plan is shared and agreed, however, the details are not clearly agreed yet.

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/

Expression thresholding

For a shared set for expression profiles to identify cellular states, we would like to set a threshold of expression (not relying on any other evidences - such as DNase HS site, since it could ignore rare cells). We will decide this until 28th Oct, 2011. The candidates are:

• 10 reads at least in a library (arbitrary choise)
• Data driven approach (Piotr will give a try)

Normalization

• Yishai and Cesare will compare the normalised data to check whether the thresholding and collapsing the cluster will impact on the normalised structure. Stick with TSS.
• Normalization check: Compare power-law method of Piotr's or Yishai with EdgeR TMM RLE and TPM.

See expression_normalization for further.

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