Information
Accession GMS-64-70 (FID: 655)Browse (ALL)
Title in situ Hi-C on primary human cardiomyocytes
HiC file 4DNFINR2MFSM (7.06 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 (323.59 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 6285 domains
11277 boundaries
GMS Loop 12585 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (11277)
CTCF(+) RAD21(-)  360 (3.19%)
CTCF(-) RAD21(+)  365 (3.24%)
CTCF(+) RAD21(+)  1546 (13.71%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 334 24.759 0.546
ZBTB2 302 19.588 0.543
Nr2e3 400 11.557 0.507
RHOXF1 423 10.755 0.516
RAX2 260 10.222 0.509
Shox2 243 9.884 0.511
ISX 235 9.878 0.509
SHOX 232 9.704 0.508
FOXL1 429 9.412 0.522
VAX1 331 8.867 0.512
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (12585 x2 anchors)
CTCF(+) RAD21(-)  514 (4.08%) LA
 527 (4.19%) RA
 27 (0.21%) LA & RA
CTCF(-) RAD21(+)  406 (3.23%) LA
 401 (3.19%) RA
 25 (0.2%) LA & RA
CTCF(+) RAD21(+)  3104 (24.66%) LA
 3232 (25.68%) RA
 1068 (8.49%) LA + RA
CTCF directionality
(12596 cases)		  963 (7.65%)Convergent ≫ ≪
 44 (0.35%)Divergent ≪ ≫
 377 (2.99%)Tandem ≫ ≫
 4631 (36.77%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF1529118.9760.605
ZBTB21375100.0930.594
Sox5224464.3560.575
RHOXF1140055.7080.519
MEIS1163451.9580.530
FOXL1147243.1510.540
NFATC288439.2530.576
FOXI1140339.0900.538
FOXO4140339.0900.537
FOXO6140339.0900.535
 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