Pan-cell type continuous chromatin state annotation of all IHEC epigenomes (from Libbrecht Lab)
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Understanding the mechanistic basis of genetic disease requires annotating the regulatory elements in the human genome. 
To this end, the International Human Epigenome Consortium (IHEC) has generated thousands of epigenomic datasets 
including ChIP-seq, DNase-seq, and ATAC-seq—that measure various biochemical activities in the genome, 
including transcription factor binding, histone modification, and DNA accessibility. 
Currently, the predominant methods for integrating these data sets to annotate regulatory elements are 
segmentation and genome annotation (SAGA) algorithms such as ChromHMM and Segway. The majority of annotations generated 
by these methods are cell type-specific. However, as the number of profiled cell types has grown into the thousands, 
using thousands of cell type-specific chromatin state annotations proves undesirable for many applications. Therefore, recently, 
researchers have sought a single unified annotation of regulatory elements across all cell types, known as a “pan-cell type” annotation. 

Here, we present a pan-cell type annotation that summarizes all IHEC epigenomes using the recently-developed method, epigenome-ssm. 
This pan-cell type annotation comprises 33 genome-wide chromatin state feature signal tracks, each of which captures a regulatory program 
driving genomic activity in one or more cell types. We show that these feature maps constitute an intuitive and visualizable summary of epigenomic data.

- ./ssm-features/*.bw: Each BigWig file contains a pan-cell type feature signal track.
- ./ssm-caas/SSM-CAAS_phyloP.bw: The SSM-CAAS signal track generated using a regression model that takes the pan-cell type features as input and predicts phyloP.

IHEC companion paper: https://www.biorxiv.org/content/10.1101/2025.02.06.636950v1
epigenome-ssm original publication: https://doi.org/10.1093/bioinformatics/btac283

Link to a UCSC Genome Browser session containing all the signal tracks: https://genome.ucsc.edu/s/habib/epigenome%2Dssm.IHEC.compact

Contact: Habib Daneshpajouh (habib.dpajouh@gmail.com), Maxwell Libbrecht (maxwl@sfu.ca)