CAGE Cluster update: Difference between revisions

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


=== 'Promotome' set ===
=== '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.
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: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/110804-dpi-clusters-expression/hg19-v1.0-RC1/110926-promotome-v1.0-RC1.pdf 110926-promotome-v1.0-RC1.pdf]

⚫
* directory: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/110804-dpi-clusters-expression
⚫
*available data: expression and human readable (but computer-generated) description for each clsuter. See method for the cluster description here: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/110804-dpi-clusters-expression/hg19-v1.0-RC1/110926-promotome-v1.0-RC1.pdf 110926-promotome-v1.0-RC1.pdf]
⚫
* '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.
⚫
*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 ===
=== Genomic coordinates ===
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[https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=od32NnsKIlWqzU3jHclziD human] and [https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=bippavM-Cxqj3r6PYf0Zz mouse]
[https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=od32NnsKIlWqzU3jHclziD human] and [https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=bippavM-Cxqj3r6PYf0Zz mouse]


=== TSS classifier ===
=== TSS classifier ===


[Sebastian et al.]
[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


⚫
*https://fantom5-collaboration.gsc.riken.jp/webdav/home/seb/update12/documentation_ud12.pdf
⚫
[Timo]
* https://fantom5-collaboration.gsc.riken.jp/webdav/home/Lassmann/TSS_classification/
*https://fantom5-collaboration.gsc.riken.jp/webdav/home/seb/update12/rescue/documentation_ud12_update.pdf


⚫
[Timo]
⚫
== Expression thresholding ==


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


⚫
== Expression thresholding ==
⚫
* 10 reads at least in a library (arbitrary choise)
⚫
* Data driven approach (Piotr will give a try)


⚫
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:
⚫
== Normalization ==


⚫
*10 reads at least in a library (arbitrary choise)
⚫
* 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.
⚫
*Data driven approach (Piotr will give a try)
⚫
* Normalization check: Compare power-law method of Piotr's or Yishai with EdgeR TMM RLE and TPM.


⚫
== Normalization ==
=== Impact of Normalization on FANTOM5 hCAGE promoterome: Implementation Plan (0.1) ===
# We (Trento, Columbia – Piotr is invited) will start implementing the normalization check scheme. It means building a generic script to run on DPI TSS tag cluster set(s) when they are ready. Can be run on any other clustering scheme for TSS, or before the clustering. Hopefully
## Run power-law fits on single libraries, compare with pooled data; check range of parameters, infer stability on pooled; compare with QC indicators on single libraries; consider; check for batch effect. Start from YB script; Piotr’s version as available.
## Match with normalization and QC methods from edgeR, also in script form. Keep it generic, automate.
## Apply on existing tag DPI clusters. Run also before and after other clustering. Prepare reporting scheme.
## Verify impact on a few examples of downstream analysis, e.g. quality/stability/accuracy of classifiers and networks
# Apply on DPI tag cluster set(s) as they are ready and report, to be used for main paper
# It can make sense to reuse all material for the “peak clustering and normalization” satellite paper to submit aside the main paper, or later


⚫
*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 [[Tag Cluster Annotation|the cluster working group]] ==

⚫
==== Method Description ====

⚫
[https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Transcript_model_derived_annotation_protocol#Promoter_annotations_of_.22UPDATE_012_Decomposition-based_Peak_Identification_.28DPI.29_cluster___.22 Transcript model derived annotation protocol]

⚫
==== Annotation Results ====


⚫
== Cluster annotations discussed in [[Tag_Cluster_Annotation|the cluster working group]] ==
⚫
==== Method Description ====
⚫
[https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Transcript_model_derived_annotation_protocol#Promoter_annotations_of_.22UPDATE_012_Decomposition-based_Peak_Identification_.28DPI.29_cluster___.22 Transcript model derived annotation protocol]
⚫
==== Annotation Results ====
*[https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/CAGE-Tag-Cluster-Annotation_Aug11/ webdav repository]
*[https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/CAGE-Tag-Cluster-Annotation_Aug11/ webdav repository]

====== Human Decomposition-based Peak Identification (DPI) cluster ======
====== 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/
*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.CpGislands.annotated.osc.gz
**tc.decompose_smoothing_merged.hg19.EST.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.non_coding.annotated.sym.osc.gz
**tc.decompose_smoothing_merged.hg19.Ensembl.protein_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.F5_human_lncRNAome.annotated.osc.gz
**tc.decompose_smoothing_merged.hg19.RefSeq.non_coding.annotated.sym.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.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.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-pseudo.annotated.sym.osc.gz
**tc.decompose_smoothing_merged.hg19.gencode.non_coding.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.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.non_coding.annotated.sym.osc.gz
**tc.decompose_smoothing_merged.hg19.knownGene.protein_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.mRNA.annotated.osc.gz
**tc.decompose_smoothing_merged.hg19.rmsk.annotated.repClass.repFamily.osc.gz
**tc.decompose_smoothing_merged.hg19.rmsk.annotated.repClass.repFamily.osc.gz


====== Mouse Decomposition-based Peak Identification (DPI) cluster ======
====== 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/
*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.CpGislands.annotated.osc.gz
**tc.decompose_smoothing_merged.mm9.EST.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.non_coding.annotated.sym.osc.gz
**tc.decompose_smoothing_merged.mm9.Ensembl.protein_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.non_coding.annotated.sym.osc.gz
**tc.decompose_smoothing_merged.mm9.RefSeq.protein_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.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.non_coding.annotated.sym.osc.gz
**tc.decompose_smoothing_merged.mm9.knownGene.protein_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.mRNA.annotated.osc.gz
**tc.decompose_smoothing_merged.mm9.rmsk.annotated.repClass.repFamily.osc.gz
**tc.decompose_smoothing_merged.mm9.rmsk.annotated.repClass.repFamily.osc.gz


<br>



== Other clusters on UPDATE_012 ==
== Other clusters on UPDATE_012 ==
Line 99: Line 99:


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


Revision as of 11:57, 21 October 2011

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.

Genomic coordinates

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

ZENBU configuration

human and mouse

TSS classifier

[Sebastian et al.]

[Timo]

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

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

Related pages

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