Information
Accession GMS-64-51 (FID: 622)Browse (ALL)
Title in situ Hi-C on primary human cardiomyocytes
HiC file 4DNFI176BGDG (7.29 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-08 12:49:26
Last update date2025-02-08 12:49:26
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 2025-02-08 12:49:26
Reference hg38 (Human)  
Result file DomainCall.tar.gz (324.21 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 6640 domains
11832 boundaries
GMS Loop 12588 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (11832)
CTCF(+) RAD21(-)  423 (3.58%)
CTCF(-) RAD21(+)  352 (2.97%)
CTCF(+) RAD21(+)  1604 (13.56%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 309 18.760 0.548
Sox5 754 16.701 0.558
ZBTB2 282 14.885 0.549
MEIS1 562 13.817 0.502
GATA3 528 10.304 0.509
HOXD4 371 10.152 0.510
HOXB6 434 9.618 0.512
RHOXF1 372 9.491 0.520
PRRX1 406 9.259 0.499
NFATC2 293 9.057 0.543
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (12588 x2 anchors)
CTCF(+) RAD21(-)  519 (4.12%) LA
 501 (3.98%) RA
 33 (0.26%) LA & RA
CTCF(-) RAD21(+)  386 (3.07%) LA
 438 (3.48%) RA
 21 (0.17%) LA & RA
CTCF(+) RAD21(+)  3121 (24.79%) LA
 3154 (25.06%) RA
 1000 (7.94%) LA + RA
CTCF directionality
(12597 cases)		  895 (7.1%)Convergent ≫ ≪
 54 (0.43%)Divergent ≪ ≫
 376 (2.98%)Tandem ≫ ≫
 4663 (37.02%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF1474112.1280.604
ZBTB2123783.6780.597
MEIS1276471.1900.514
FOXL1150948.6890.532
FOXP3143845.2450.526
FOXO6143445.2260.531
FOXI1143345.1420.535
FOXO4143345.1420.532
RHOXF1120542.3420.519
NFATC295140.4300.575
 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