UCSC Genome Browser Sessions (Figure 2 and Supplemental Figures S5-6)

ChIA-PET loops' anchors and Enhancer/Promoter regions were resized to 1000 bp relative to their center. Please refer to the 'CT-FOCS predicted enhancer-promoter interactions' table below for the original sizes.


CT-FOCS predicted cell type-specific enhancer-promoter interactions

Name (link) Species Description Type Size
FANTOM5 cell type-specific Enhancer-Promoter links with annotations Human (hg19) A tab-delimited text file. see README file for description in additional data below txt 39MB
ENCODE cell type-specific Enhancer-Promoter links with annotations Human (hg19) A tab-delimited text file. see README file for description in additional data below txt 3MB
Roadmap Epigenomics cell type-specific Enhancer-Promoter links with annotations Human (hg19) A tab-delimited text file. see README file for description in additional data below txt 3MB

FANTOM5 data - Human (hg19)

Name (link) Description Type Size
Promoter-TSSs RLE profiles A matrix: rows are promoter-TSSs, columns are samples (Library id) rds 35MB
Promoter genomic positions (genome build: hg19) A GRanges object: entries are promoter-TSSs, each entry contains chromosome, start and end positions, name, and more rds 750KB
Sample annotation A matrix: rows are samples, columns represent sample information (lib_id, cell_type, lib_size, and more) rds 44KB
Promoter-TSS's candidate enhancers in a fixed window A list: entries are Promoter-TSSs. Each entry contains the set of enhancer names within a fixed window around the Promoter-TSS rds 1.7MB
Enhancer-TSSs RLE profiles A matrix: rows are enhancer-TSSs, columns are samples (Library id) rds 8.3MB
Enhancer genomic positions (genome build: hg19) A GRanges list: entries are enhancer-TSSs, each entry contains chromosome, start and end positions, name, and score rds 604KB
ChIA-PET connected loop sets (CLSs) for GM12878 A list: entries are Promoter-TSSs. Each entry contains an n-vector (n=number of candidate enhancers) with TRUE/FALSE, where TRUE is an EP link supported by ChIA-PET CLS. rds 1.9MB
Enhancer-Promoter links per cell type A list. Each entry of a cell type is a list of promoter-TSSs, each is a vector of enhancer names in enhancer GRanges list rds 2.75MB

ENCODE data - Human (hg19)

Name (link) Description Type Size
Promoter-DHSs count profiles A matrix: rows are promoter-DHSs, columns are GEO samples rds 21.5MB
Promoter-DHSs RLE (log2) profiles A matrix: rows are promoter-DHSs, columns are GEO samples rds 139MB
Promoter-DHSs RLE profiles A matrix: rows are promoter-DHSs, columns are GEO samples rds 27.4MB
Promoter genomic positions (genome build: hg19) A GRanges object: entries are promoter-DHSs, each entry contains chromosome, start and end positions, name, and more rds 4.3MB
Sample annotation A matrix: rows are samples, columns represent sample information (GEO_id, cell_type, lib_size, and more) rds 5.6KB
Promoter-DHS's candidate enhancers in a fixed window A list: entries are Promoter-DHSs. Each entry contains the set of enhancer indices within a fixed window around the Promoter-DHS rds 15MB
Enhancer-DHSs count profiles A matrix: rows are enhancer-DHSs, columns are GEO samples rds 109MB
Enhancer-DHSs RLE (log2) profiles A matrix: rows are enhancer-DHSs, columns are GEO samples rds 139MB
Enhancer-DHSs RLE profiles A matrix: rows are enhancer-DHSs, columns are GEO samples rds 139MB
Enhancer genomic positions (genome build: hg19) A GRanges list: entries are enhancer-DHSs, each entry contains chromosome, start and end positions, name, and score rds 11MB
ChIA-PET connected loop sets (CLSs) for GM12878 A list: entries are Promoter-DHSs. Each entry contains an n-vector (n=number of candidate enhancers) with TRUE/FALSE, where TRUE is an EP link supported by ChIA-PET CLS. rds 16.4MB
Enhancer-Promoter links per cell type A list. Each entry of a cell type is a list of promoter-DHSs, each is a vector of enhancer names in enhancer GRanges list rds 223KB

Roadmap Epigenomics data - Human (hg19)

Name (link) Description Type Size
Promoter-DHSs count profiles A matrix: rows are promoter-DHSs, columns are GEO samples rds 17.8MB
Promoter-DHSs RLE (log2) profiles A matrix: rows are promoter-DHSs, columns are GEO samples rds 78.5MB
Promoter-DHSs RLE profiles A matrix: rows are promoter-DHSs, columns are GEO samples rds 65MB
Promoter genomic positions (genome build: hg19) A GRanges object: entries are promoter-DHSs, each entry contains chromosome, start and end positions, name, and more rds 2.4MB
Sample annotation A matrix: rows are samples, columns represent sample information (GEO_id, cell_type, lib_size, and more) rds 7.8KB
Promoter-DHS's candidate enhancers in a fixed window A list: entries are Promoter-DHSs. Each entry contains the set of enhancer indices within a fixed window around the Promoter-DHS rds 6.8MB
Enhancer-DHSs count profiles A matrix: rows are enhancer-DHSs, columns are GEO samples rds 149MB
Enhancer-DHSs RLE (log2) profiles A matrix: rows are enhancer-DHSs, columns are GEO samples rds 846MB
Enhancer-DHSs RLE profiles A matrix: rows are enhancer-DHSs, columns are GEO samples rds 572MB
Enhancer genomic positions (genome build: hg19) A GRanges list: entries are enhancer-DHSs, each entry contains chromosome, start and end positions, name, and score rds 9.6MB
Enhancer-Promoter links per cell type A list. Each entry of a cell type is a list of promoter-DHSs, each is a vector of enhancer names in enhancer GRanges list rds 258KB

Additional data: analysis and external databases

Name (link) Description Type Size
README Describes the fields within each interactions.txt file txt 1KB
HOCOMOCOv11 Human PWM core annotation [1] A tsv file tsv 76KB
Auxiliary data for integrative analysis A zip file: contains .rds files of ChIA-PET interactions [2-3], digital genomic footprints (DGFs) [4], HOCOMOCOv11 Human PWM core annotation [1], and ENCODE gene expression data [5]. Positions are in hg19 genome build. zip 87MB
Intermediate files for creating the paper's figures, and for inferring cell type-specific EP links A zip file with .rds files zip 704KB

[1] Kulakovskiy I V, Vorontsov IE, Yevshin IS, Sharipov RN, Fedorova AD, Rumynskiy EI, et al. HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. Nucleic Acids Res. Oxford University Press; 2017;46:D252-D259
[2] Tang Z, Luo OJ, Li X, Zheng M, Zhu JJ, Szalaj P, et al. CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. Cell [Internet]. Elsevier Inc.; 2015;163:1611–27. Available from: http://dx.doi.org/10.1016/j.cell.2015.11.024
[3] Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. Elsevier; 2012;148:84–98
[4] Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature. 2012;489:83–90
[5] Sheffield NC, Thurman RE, Song L, Safi A, Stamatoyannopoulos JA, Lenhard B, et al. Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. Genome Res. 2013;23:777–88