Candidate cis-regulatory elements, or cCREs, colored by dominant epigenetic state This composite track displays the cCREs colored by the dominant epigenetic state found in that cCRE in each cell type (Xiang et al. 2024). Related resources in this track hub are the track cCREs, which is a compilation of all cCREs discovered in human blood cell types in the VISION project along with annotation of conservation and cross-cell type clustering, and the composite track IDEAS human-mouse, which has the epigenetic state assignments genome-wide across human blood cell types resulting from jointly analyzing the data in human and mouse. A guide to the epigenetic states is on the Track Settings page of the IDEAS human-mouse composite track.
In "dense" mode, the display shows the position of each cCRE, which is colored to indicate the epigenetic state that occupies the greatest portion of the cCRE in each cell type. The color codes are defined in the Description section. In "pack" or "full" mode, the genomic intervals are further annotated with the shorthand for the function commonly associated with the combination of epigenetic features that make up the state. These include P for promoter and E for enhancer. The full listing is on the Track Settings page of the IDEAS human-mouse composite track.
The track names (short name and the end of the long name) give an abbreviation for the blood cell type and the biosamples from the Blueprint Consortium (replicates are from different donors) or the file id after downloading and processing other published data (100xxx). The cell types are HSC = hematopoietic stem cell, MPP = multipotent progenitor cell, LMPP = lymphoid-myeloid primed progenitor cell, CMP = common myeloid progenitor, MEP = megakaryocyte erythrocyte progenitor, GMP = granulocyte monocyte progenitor, CLP = common lymphoid progenitor, CD34_E = erythroblasts generated by in vitro differentiation of CD34+ HSCs, ERY = erythroblast, MK = megakaryocyte, EOS = eosinophil, MONp = primary monocyte, MONc = classical monocyte, NEU = neutrophil, B = B cell, NK = natural killer cell, T_CD4 = CD4+ T cell, T_CD8 = CD8+ T cell, HUDEP = immortalized human umbilical cord blood—derived erythroid progenitor cell lines expressing fetal globin genes (HUDEP1) or adult globin genes (HUDEP2), K562 = a human cancer cell line with some features of early megakaryocytic and erythroid cells. AVE is a track with state assignments based on the average signal for each epigenetic feature across cell types.
The use of IDEAS in the IS mode for peak calling on chromatin accessibility data was described in Xiang et al. 2021 and Xiang et al. 2024. The multi-feature IDEAS segmentation on human and mouse epigenomes was described in Xiang et al. 2024.
The data normalization, the peak calls using IDEAS in the IS mode, and generation of the multi-feature IDEAS segmentation on human and mouse epigenomes were done by Guanjue Xiang. The data downloads, re-mapping and processing, generation of the tracks displayed, and development of the track hub were done by Belinda Giardine.
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, Keller CA, Giardine B, An L, Li Q, Zhang Y, Hardison RC. S3norm: simultaneous normalization of sequencing depth and signal-to-noise ratio in epigenomic data. Nucleic Acids Res. 2020 May 7;48(8):e43. doi:10.1093/nar/gkaa105. PMID: 32086521; PMCID: PMC7192629.
Xiang G, Giardine BM, Mahony S, Zhang Y, Hardison RC. S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types. Bioinformatics. 2021 Sep 29;37(18):3011-3013. doi:10.1093/bioinformatics/btab148. PMID: 33681991; PMCID: PMC8479670.
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.
These data are available for use without restrictions.
Ross Hardison rch8@psu.edu