cell type specific enhancers

Question

[alessandrotestori7]

Hi! What resources are available to predict putative target genes of a set of enhancer regions in a cell type specific manner from public data? My only input is a file with genomic regions that I want to explore. Thanks!

Edit: The coordinates are from ATAC-seq... I was hoping there would be the possibility to filter those regions for active enhancers and then identify target genes through public cell type specific data

Answer 1

[GouthamAtla]

I am not sure about cell-types, but you can try to get tissue type from encode epigenome roadmap data. They have clustered all "enhancer" states from chromHmm across tissues and you can access the data here . With this you can checkif your enhancer are particularly enriched in any tissue type.

Bases on above enrichments, you can dig literature for "Hi-C" like data for that particular tissue.

A source to infer the enhancer interaction is would be Jung et al, Nat Genetics.

If you mention what tissue you are working with, someone will be able to provide if there is any scATAC datasets for that tissue which might help with Cell-Type specificity.

[alessandrotestori7]

Sounds like a good strategy, thank you! BTW, I am working with human dendritic cells

Answer 2

[ATpoint]

I recently came across FOCS a collection of enhancer/promoter pair predictions that relies on integration of CAGE-seq and ENCODE epigenomic data. They provide lists with cross-validated E-P pairs that might be worth a look. As always with these predictions be aware that no method is perfect and it should be used to build hypotheses that are then to be confirmed with additonal data/experiments. Predictions exist for hg19 and mm9 but liftOver is always an option.

Website with download section:http://acgt.cs.tau.ac.il/focs/

Paper at Genome Biology: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5930446/

[alessandrotestori7]

FOCS seems to be a good resource - thank you!