Information
Accession GMS-64-75 (FID: 662)Browse (ALL)
Title in situ Hi-C on primary human cardiomyocytes
HiC file 4DNFI6PD831D (8.35 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-18 15:23:12
Last update date2025-02-18 15:23:12
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 15:23:12
Reference hg38 (Human)  
Result file DomainCall.tar.gz (329.04 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 6761 domains
11965 boundaries
GMS Loop 13436 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (11965)
CTCF(+) RAD21(-)  434 (3.63%)
CTCF(-) RAD21(+)  377 (3.15%)
CTCF(+) RAD21(+)  1738 (14.53%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 361 26.370 0.545
Sox5 797 26.140 0.560
ZBTB2 353 25.080 0.542
ZNF354C 497 22.614 0.472
RHOXF1 466 19.748 0.519
FOXL1 490 17.560 0.515
MEIS1 431 16.102 0.499
FOXP3 462 15.862 0.520
FOXI1 460 15.821 0.526
FOXO4 460 15.821 0.522
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (13436 x2 anchors)
CTCF(+) RAD21(-)  621 (4.62%) LA
 647 (4.82%) RA
 28 (0.21%) LA & RA
CTCF(-) RAD21(+)  390 (2.9%) LA
 397 (2.95%) RA
 14 (0.1%) LA & RA
CTCF(+) RAD21(+)  3452 (25.69%) LA
 3391 (25.24%) RA
 1096 (8.16%) LA + RA
CTCF directionality
(13446 cases)		  997 (7.41%)Convergent ≫ ≪
 48 (0.36%)Divergent ≪ ≫
 468 (3.48%)Tandem ≫ ≫
 5105 (37.97%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF1757135.3380.604
ZBTB21549110.7250.598
Sox5251380.9880.580
FOXL1167462.8860.530
FOXO4159662.0770.533
FOXI1159761.7780.538
FOXO6159761.7780.534
FOXP3160261.4510.529
MEIS1178760.6330.520
Arid3a126851.8410.590
 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