Description

Gene-cCRE pairs
This composite track displays predicted gene-candidate cis-regulatory element (cCRE) pairs in mouse hematopoietic cell types, generated as part of the VISION project (ValIdated Systematic IntegratiON of hematopoietic epigenomes). The pairs link genes to their predicted distal regulatory elements using epigenetic-state Regulatory Potential (esRP) scores.

The track contains subtracks for individual cell types, each showing gene-cCRE interactions scored by esRP in that cell type, as well as a combined track showing pairs across all cell types scored by correlation. The cell types represented include:

All cell types

Gene-cCRE pairs across all cell types with correlation-based scores.

Hematopoietic progenitors

LSK (lineage-negative Sca1-positive Kit-positive), CMP (common myeloid progenitor), GMP (granulocyte-monocyte progenitor), CLP (common lymphoid progenitor), CFU-E (colony-forming unit erythroid), CFU-MK (colony-forming unit megakaryocyte).

Erythroid cells

ERY (adult erythroblasts), ERY fetal liver, G1E, G1E-ER4+E2 (estradiol-treated).

Megakaryocytes

MK mature (fetal liver), MK immature (adult).

Myeloid cells

MONO (monocytes), NEU (neutrophils).

Lymphoid cells

B (splenic B cells), NK (natural killer cells), T CD4 (CD4+ T cells), T CD8 (CD8+ T cells).

Cell lines

HPC7 (hematopoietic progenitor cell line).

Display Conventions and Configuration

Gene-cCRE pairs are displayed as interaction arcs connecting genes to their predicted regulatory elements using the bigInteract format. The score reflects the esRP value for cell-type-specific subtracks or the correlation score for the combined track. Higher scores indicate stronger predicted regulatory relationships.

Methods

Gene-cCRE pairs were identified by computing epigenetic-state Regulatory Potential (esRP) scores, which integrate chromatin state information across multiple epigenomic marks to predict regulatory element activity in each cell type. Candidate cis-regulatory elements (cCREs) were defined by the IDEAS joint segmentation, and pairs were formed by linking each cCRE to nearby genes based on the esRP score in each cell type. The combined track uses correlation of esRP scores across cell types.

Credits

Guanjue Xiang developed the esRP scoring method. Belinda Giardine generated the tracks displayed and developed the track hub.

References

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