Retinal pigment mesenchyme transition: Difference between revisions

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* [https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=egQcRvVcGltnph4I4lELw;loc=hg19::chr19:36376423..36402712 ARPE-19 timecourse - update Oct 26th]
* [https://fantom5-collaboration.gsc.riken.jp/zenbu/gLyphs/#config=egQcRvVcGltnph4I4lELw;loc=hg19::chr19:36376423..36402712 ARPE-19 timecourse - update Oct 26th]


'''Gene expression profiles'''
'''Expression profiles'''
*Known gene expression for the retinal epithelium series
*Gene and CAGE cluster expression for the retinal epithelium series
* [https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/20111008_expression_table_by_timecourse/human_ARPE-19.hCAGE.hg19.tpm.refgene.osc.txt.gz TPM]
*https://fantom5-collaboration.gsc.riken.jp/webdav/home/arner/timecourse/time_course_main_paper_freeze_feb2013/qc_release_130226/human_ARPE-19/expression_tables/
* [https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/20111008_expression_table_by_timecourse/human_ARPE-19.hCAGE.hg19.count.refgene.osc.txt.gz tagcount]
*Promoterome v1.0 expression for the ARPE-19 series
*Top dynamic TFs in the ARPE-19 series
*Freeze1 cluster based RLE normalized expression
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/20120612_cluster_expression_table_by_timecourse/human_ARPE-19.hCAGE.hg19.RLE.tpm.cluster.txt.gz
** Cluster to gene association https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/20120612_cluster_expression_table_by_timecourse/human_robust_cluster2entrez.txt

'''Motifs'''
*Top dynamic motifs in the ARPE-19 series


'''MARA based network results'''
'''MARA based network results'''
⚫
*https://fantom5-collaboration.gsc.riken.jp/webdav/home/arner/timecourse/time_course_main_paper_freeze_feb2013/qc_release_130226/human_ARPE-19/mara/
*Most recent version (July 23 2012):
⚫
**https://fantom5-collaboration.gsc.riken.jp/webdav/home/arner/timecourse/release_120723/human_ARPE-19/human_ARPE-19.mara
**https://fantom5-collaboration.gsc.riken.jp/webdav/home/arner/timecourse/release_120723/human_ARPE-19/human_ARPE-19.net.tf_gene.csv
**https://fantom5-collaboration.gsc.riken.jp/webdav/home/arner/timecourse/release_120723/human_ARPE-19/human_ARPE-19.net.tf_prom.csv


'''Related samples'''
'''Related samples'''
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'''Quality control'''
'''Quality control'''

*Most recent version (July 23 2012):
**https://fantom5-collaboration.gsc.riken.jp/webdav/home/arner/timecourse/release_120723/human_ARPE-19/
https://fantom5-collaboration.gsc.riken.jp/webdav/home/arner/timecourse/time_course_main_paper_freeze_feb2013/qc_release_130226/human_ARPE-19/


==[[ISMARA]] analysis results==
==[[ISMARA]] analysis results==

Revision as of 14:44, 27 February 2013

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Zenbu configurations and status

Expression profiles

MARA based network results

Related samples

  • ...

References

  • ...

Quality control

https://fantom5-collaboration.gsc.riken.jp/webdav/home/arner/timecourse/time_course_main_paper_freeze_feb2013/qc_release_130226/human_ARPE-19/

ISMARA analysis results

All samples: http://ismara.unibas.ch/timecourses/retinal_pigment_EMT/ismara_report/index.html

Replicate averaged: http://ismara.unibas.ch/timecourses/ARPE19-avgd/averaged_report/index.html

For more information, see ISMARA.

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