Retinal pigment mesenchyme transition

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Zenbu configurations and status

• ARPE-19
• ARPE-19 timecourse - update Oct 26th

Gene expression profiles

• Known gene expression for the retinal epithelium series
• TPM
• 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

• 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

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References

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Quality control

• Most recent version (July 23 2012):
  • https://fantom5-collaboration.gsc.riken.jp/webdav/home/arner/timecourse/release_120723/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.