Q:
I am very familiar with the ENCODE TF datasets, as I’ve been applying it to various problems in my PhD. I was interested in the expression analysis across human tissues for the ((miR –> TF) –> targets) FFL. There is a reference in the Supplementary file (section H) to the protein-coding expression atlas Su et al. 2004, for the TF and protein-coding targets in this loop, but doesn’t seem to be a ref for the corresponding expression data for miRNAs? I assume it would be Landgraf et al. 2007 ‘A mammalian microRNA expression atlas based on small RNA library sequencing’, since this allows matched tissues and samples with Su et al. However, it might be some other dataset. It would be helpful to be able to replicate/extend the FFL analysis using the correct data. Would you be able to forward this email to the relevent person(s) to confirm whether microRNA expression was taken from Landgraf atlas? Many thanks for your help

Slight correction: The FFL studied for expression pattern of
components is the other way round: ((TF –> miR) –> targets).

A:
the miRNA expression is actually from
Lu et al, Nature 2005
http://www.nature.com/nature/journal/v435/n7043/full/nature03702.html

if you go to
http://www.broadinstitute.org/cgi-bin/cancer/datasets.cgi
under the heading "MicroRNA Expression Profiles Classify Human Cancers"
see files

Common_miRNA.gct
and
Common_Affy.zip