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pchic_blood_cells — Promoter Capture Hi-C in 17 human blood cell types (2016)

Description

Networks of chromatin contacts between promoters and other regions of the human genome, measured with Promoter Capture Hi-C (PCHi-C) in 17 types of primary blood cells (and their progenitors) by Javierre et al., to link enhancers and non-coding disease variants to the genes they regulate. In Hi-C, the DNA of the cells is cross-linked, cut with the restriction enzyme HindIII, and ligated, so that pairs of fragments that are close in the three-dimensional nucleus are sequenced together; in Capture Hi-C, the ligation products are enriched for the fragments that contain a promoter (the "baits", fragments that contain annotated promoters). Significant interactions were called with CHiCAGO, whose score (a soft-thresholded $-\log$ $p$-value) is given per cell type.

Nodes are HindIII restriction fragments of the genome (GRCh37 assembly), and a directed edge goes from a bait to a fragment it interacts with (the "other end"), with the CHiCAGO scores of the interaction in the cell types. Interactions between two baits are detected from the point of view of each bait, so that they can appear in both directions.

  • cutoff5: the interactions with a score of at least 5 (the threshold of the study) in at least one cell type.
  • cutoff0: all the interactions with a positive score in at least one cell type (the unthresholded data).
  • reciprocal_cutoff0: the interactions of the reciprocal capture experiment, in which fragments that interact with promoters (mostly enhancers) were captured as baits, in four cell types (megakaryocytes, erythroblasts, activated and non-activated CD4+ T cells), with a positive score in at least one of them.
  • pchic_vs_rchic: the interactions between the baits of PCHi-C and the baits of the reciprocal capture, with their scores in both experiments, from the point of view of PCHi-C (edges go from the PCHi-C bait to the reciprocal bait), for the four cell types of the reciprocal capture.

The cell types (abbreviations of the score properties) are: Mon (monocytes), Mac0, Mac1, Mac2 (macrophages M0, M1 and M2), Neu (neutrophils), MK (megakaryocytes), EP (endothelial precursors), Ery (erythroblasts), FoeT (fetal thymus), nCD4, tCD4, aCD4, naCD4 (naive, total, activated and non-activated CD4+ T cells), nCD8, tCD8 (naive and total CD8+ T cells), nB, tB (naive and total B cells).

The networks have the following properties:

  • (Node) fragment_id: the identifier of the restriction fragment (from the restriction map of the capture design).
  • (Node) chr, start, end: the chromosome and the coordinates of the fragment (GRCh37).
  • (Node) genes: the genes whose promoters are in the fragment, separated by ; (Ensembl release 75; empty for fragments without annotated promoters).
  • (Node) is_bait: whether the fragment is a bait of the experiment (in pchic_vs_rchic: a PCHi-C bait).
  • (Edge) dist: the distance between the bait and the other end (positive if the bait is upstream of the other end; NaN for interactions between chromosomes).
  • (Edge) Mon, Mac0, ..., tB: the CHiCAGO scores of the interaction in each cell type (in pchic_vs_rchic: PCHiC_MK, ..., rCHiC_MK, ... for the two experiments).
  • (Edge) cluster_id, cluster_post_prob (cutoff5): the cluster of the interaction in the clustering of the interactions by their scores across cell types (with AutoClass, Figure 2B of the paper), and the posterior probability of the assignment.
  • (Edge) is_b2b (reciprocal_cutoff0): whether the interaction is between two baits.
Tags
Biological Genetic Weighted Metadata
Added
2026-10-31
Citation
  • B. M. Javierre, O. S. Burren, S. P. Wilder, R. Kreuzhuber, S. M. Hill, S. Sewitz, J. Cairns, S. W. Wingett, C. Várnai, M. J. Thiecke, et al., "Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters." Cell 167, 1369-1384.e19 (2016) 10.1016/j.cell.2016.09.037 Sci-Hub
Upstream URL OK
https://osf.io/u8tzp/
https://www.chicp.org/
Upstream license
Creative Commons Attribution 4.0 International (CC BY 4.0), https://creativecommons.org/licenses/by/4.0/
Networks
Tip: click on a column header to sort the list, or hover over it for a description.
Column legend
$\left<k\right>$
Mean degree
$\sigma_k$
Standard deviation of the degrees
$\lambda_h$
Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$
Random walk mixing time
$r$
Degree assortativity
$c$
Global clustering coefficient
$\oslash$
(Pseudo-) diameter
$S$
Relative size of the largest component
NPs
Node properties
EPs
Edge properties
Name Nodes Edges $\left<k\right>$ $\sigma_k$ $\lambda_h$ $\tau$ $r$ $c$ $\oslash$ $S$ Kind Mode NPs EPs gt GraphML GML csv
cutoff5 253,148 728,838 2.88 17.07 82.00 14964.75 -0.23 0.09 28 0.98 Directed Unipartite fragment_id chr start end genes is_bait dist Mon Mac0 Mac1 Mac2 Neu MK EP Ery FoeT nCD4 tCD4 aCD4 naCD4 nCD8 tCD8 nB tB cluster_id cluster_post_prob 89.6 MiB 107.6 MiB 106.3 MiB 100.2 MiB
cutoff0 769,334 10,554,701 13.72 88.44 243.53 5477.64 -0.70 0.11 12 1.00 Directed Unipartite fragment_id chr start end genes is_bait dist Mon Mac0 Mac1 Mac2 Neu MK EP Ery FoeT nCD4 tCD4 aCD4 naCD4 nCD8 tCD8 nB tB 744.1 MiB 914.0 MiB 896.3 MiB 874.3 MiB
reciprocal_cutoff0 275,768 796,752 2.89 63.66 283.54 5350.28 -0.41 0.03 11 1.00 Directed Unipartite fragment_id chr start end genes is_bait dist aCD4 naCD4 MK Ery is_b2b 22.1 MiB 28.5 MiB 27.7 MiB 27.5 MiB
pchic_vs_rchic 13,584 53,319 3.93 21.73 87.62 2331.45 -0.26 0.02 20 1.00 Directed Unipartite fragment_id chr start end genes is_bait dist PCHiC_MK PCHiC_Ery PCHiC_aCD4 PCHiC_naCD4 rCHiC_MK rCHiC_Ery rCHiC_aCD4 rCHiC_naCD4 1.9 MiB 2.5 MiB 2.5 MiB 2.3 MiB