Information
Accession GMS-64-75 (FID: 663)Browse (ALL)
Title in situ Hi-C on primary human cardiomyocytes
HiC file 4DNFII9NVNO3 (9.23 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 (336.74 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 6960 domains
12244 boundaries
GMS Loop 14481 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (12244)
CTCF(+) RAD21(-)  383 (3.13%)
CTCF(-) RAD21(+)  438 (3.58%)
CTCF(+) RAD21(+)  1665 (13.6%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 372 27.002 0.537
ZBTB2 355 24.309 0.534
ZNF354C 544 23.250 0.462
Sox5 814 23.190 0.560
MEIS1 625 20.482 0.504
FOXL1 528 18.240 0.515
Arid3a 412 17.769 0.532
FOXI1 499 16.681 0.523
FOXO4 499 16.681 0.520
FOXP3 499 16.681 0.517
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (14481 x2 anchors)
CTCF(+) RAD21(-)  623 (4.3%) LA
 637 (4.4%) RA
 36 (0.25%) LA & RA
CTCF(-) RAD21(+)  446 (3.08%) LA
 447 (3.09%) RA
 22 (0.15%) LA & RA
CTCF(+) RAD21(+)  3585 (24.76%) LA
 3563 (24.6%) RA
 1166 (8.05%) LA + RA
CTCF directionality
(14492 cases)		  1036 (7.15%)Convergent ≫ ≪
 53 (0.37%)Divergent ≪ ≫
 496 (3.42%)Tandem ≫ ≫
 5260 (36.3%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF152496.5840.602
Sox5280795.4230.577
ZBTB2145889.6190.584
FOXL1185364.4870.527
FOXP3176962.4690.525
FOXI1176962.0860.535
FOXO4176962.0860.532
FOXO6176962.0860.531
RHOXF1145556.5350.520
Nr2e3164053.0530.518
 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