Description

Epigenetic state Regulatory Potential
This super track groups tracks related to the epigenetic state Regulatory Potential (esRP) in mouse as part of the VISION project (ValIdated Systematic IntegratiON of hematopoietic epigenomes). The esRP score estimates the contribution of a candidate cis-regulatory element (cCRE) to the level of expression of a target gene. It is derived from beta coefficients that relate the proportion of cCRE intervals in a particular multi-feature epigenetic state to expression levels of target genes in a multivariate linear regression (Xiang et al. 2024).

This super track contains the following composite tracks:

Beta coefficients

The beta coefficient scores over the full genome. Beta coefficients estimate the contribution of each of the 25 epigenetic states to the level of expression of target genes, as determined from a multivariate regression of epigenetic states in cCREs across cell types against the level of target gene expression across cell types.

esRP

The esRP scores for cCREs in each cell type. The esRP score is a weighted sum of beta coefficients of states that cover a cCRE in a cell type, where the weights are the region covered by different states.

Methods

The epigenetic states were determined using the IDEAS genome segmentation and annotation system in a joint analysis of human and mouse blood cell epigenomes (Xiang et al. 2024). The beta coefficients were estimated by multivariate regression of epigenetic states across cell types against the level of target gene expression across cell types (Xiang et al. 2020 and 2024). The esRP scores were calculated as the weighted sum of beta coefficients of states covering each cCRE, where the weights are the proportion of the cCRE covered by each state.

Credits

Guanjue Xiang performed the multivariate regression, determined the beta coefficients, and calculated the esRP scores. Belinda Giardine calculated the beta coefficients genome-wide, generated the tracks displayed, and developed the track hub.

References

Xiang G, Keller CA, Heuston E, Giardine BM, An L, Wixom AQ, Miller A, Cockburn A, Sauria MEG, Weaver K, Lichtenberg J, Göttgens B, Li Q, Bodine D, Mahony S, Taylor J, Blobel GA, Weiss MJ, Cheng Y, Yue F, Hughes J, Higgs DR, Zhang Y, Hardison RC. An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis. Genome Res. 2020 Mar;30(3):472-484. PMID: 32132109; PMCID: PMC7111515.

Xiang G, He X, Giardine BM, Isaac KJ, Taylor DJ, McCoy RC, Jansen C, Keller CA, Wixom AQ, Cockburn A, Miller A, Qi Q, He Y, Li Y, Lichtenberg J, Heuston EF, Anderson SM, Luan J, Vermunt MW, Yue F, Sauria MEG, Schatz MC, Taylor J, Göttgens B, Hughes JR, Higgs DR, Weiss MJ, Cheng Y, Blobel GA, Bodine DM, Zhang Y, Li Q, Mahony S, Hardison RC. Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Genome Res. 2024 Aug 20;34(7):1089-1105. PMID: 38951027; PMCID: PMC11368181.

Data Release Policy

These data are available for use without restrictions.

Contact

Ross Hardison rch8@psu.edu