Information
Accession GMS-64-70 (FID: 656)Browse (ALL)
Title in situ Hi-C on primary human cardiomyocytes
HiC file 4DNFIJUUK1C8 (6.52 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-18 15:18:29
Last update date2025-02-18 15:18:29
Contact Sung-Joon PARK
park AT hgc.jp
The University of Tokyo
Sharingopen access
Keywords Hi-C  4DN  contact matrix 
 Domain/Loop Calling Information

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Submit date 2025-02-18 15:18:29
Reference hg38 (Human)  
Result file DomainCall.tar.gz (314.79 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 6267 domains
11234 boundaries
GMS Loop 11988 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (11234)
CTCF(+) RAD21(-)  439 (3.91%)
CTCF(-) RAD21(+)  322 (2.87%)
CTCF(+) RAD21(+)  1547 (13.77%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 296 18.807 0.537
Sox5 701 18.305 0.558
ZBTB2 254 12.679 0.540
FOXL1 432 12.266 0.515
RHOXF1 378 12.071 0.512
FOXP3 415 11.419 0.518
HOXB6 435 11.227 0.516
FOXI1 412 11.112 0.523
FOXO6 412 11.112 0.520
FOXO4 411 11.010 0.521
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (11988 x2 anchors)
CTCF(+) RAD21(-)  466 (3.89%) LA
 479 (4%) RA
 25 (0.21%) LA & RA
CTCF(-) RAD21(+)  439 (3.66%) LA
 436 (3.64%) RA
 19 (0.16%) LA & RA
CTCF(+) RAD21(+)  3062 (25.54%) LA
 3178 (26.51%) RA
 1044 (8.71%) LA + RA
CTCF directionality
(11998 cases)		  912 (7.6%)Convergent ≫ ≪
 46 (0.38%)Divergent ≪ ≫
 397 (3.31%)Tandem ≫ ≫
 4495 (37.46%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF1574133.1980.606
ZBTB2128195.5050.600
Sox5214272.9950.575
FOXL1141059.1580.537
FOXI1133655.3310.542
FOXO4133655.3310.533
FOXO6133655.3310.538
FOXP3133655.3310.534
RHOXF1120548.6350.524
MEIS1152547.1000.512
 CTCF&RAD21 in Loop Anchors
 CTCF directionality
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
 Figures
APA (5K)
 normedAPA (5K)
 centerNormedAPA (5K)
 rankAPA (5K)
APA (10K)
 normedAPA (10K)
 centerNormedAPA (10K)
 rankAPA (10K)
APA (25K)
 normedAPA (25K)
 centerNormedAPA (25K)
 rankAPA (25K)
%>4DN_get_insulation_scores_and_boundaries --bweak 0.2 --bstrong 0.5 --cutoff 2 --pixels_frac 0.66
  "--binsize 5000 --window 100000,--binsize 10000 --window 100000"

%>java -Xmx32g -jar /usr/proj/gmsuite/TOOL/Juicer/scripts/common/juicer_tools.jar arrowhead --ignore-sparsity --threads 4 -k KR -m 2000

%>java -Xmx32g -jar /usr/proj/gmsuite/TOOL/Juicer/scripts/common/juicer_tools.jar hiccups --ignore-sparsity --cpu --threads 4 -k KR -m 1024 -f .1,.1,.1 -p 4,2,1 -i 7,5,3 -t 0.02,1.5,1.75 -d 20000,20000,50000 -r 5000,10000,25000

%>java -Xmx32g -jar /usr/proj/gmsuite/TOOL/Juicer/scripts/common/juicer_tools.jar apa --ignore-sparsity --threads 4

%>hicDetectLoops --threads 2 --peakWidth 2 --windowSize 5 --pValuePreselection 0.1 --peakInteractionsThreshold 10 --obsExpThreshold 1.5 --pValue 0.025 --maxLoopDistance 2000000 --threadsPerChromosome 1 --expected mean

%>cooltools insulation --ignore-diags 2 --append-raw-scores --min-frac-valid-pixels 0.66 --min-dist-bad-bin 0 --chunksize 2000000
  win= 100000

Creating GMS_Domains.bedpe: "hicMergeDomains" with all Strong boundaries of 4DN and "intersectBed" -a all_ArrowHeads -b Strong_boundaries
%>hicMergeDomains --value 5000

Creating GMS_Loops.bedgraph: "hicMergeLoops" of hicCups merged_loops + all_hicDetectLoops -r 25000
%>hicMergeLoops -r 25000

CTCF&RAD21
%>gimme scan -gc -f 0.1 -b -N 1
Boundaries
%>gimme motifs -b genomic -s 0 -f 0.2 -t Homer --known -p JASPAR2020_vertebrates -N 1
Loops
%>gimme motifs -b genomic -s 5000 -f 0.2 -t Homer --known -p JASPAR2020_vertebrates -N 1