Information
Accession GMS-64-77 (FID: 667)Browse (ALL)
Title in situ Hi-C on an allelic series of iPSCs differentiated to cardiac cells
HiC file 4DNFIG6NF7VN (8.67 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-18 15:29:31
Last update date2025-02-18 15:29:31
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 15:29:31
Reference hg38 (Human)  
Result file DomainCall.tar.gz (450.89 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 11006 domains
18589 boundaries
GMS Loop 30458 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (18589)
CTCF(+) RAD21(-)  517 (2.78%)
CTCF(-) RAD21(+)  685 (3.68%)
CTCF(+) RAD21(+)  2698 (14.51%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 607 35.901 0.549
ZBTB2 494 22.595 0.546
Sox5 1135 17.728 0.547
Arid3a 574 17.067 0.546
RHOXF1 609 10.892 0.509
GATA3 753 9.277 0.510
HOXB1 591 9.047 0.507
TEAD3 726 9.022 0.498
ISX 401 8.400 0.503
Nobox 471 8.090 0.508
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (30458 x2 anchors)
CTCF(+) RAD21(-)  1481 (4.86%) LA
 1456 (4.78%) RA
 89 (0.29%) LA & RA
CTCF(-) RAD21(+)  1017 (3.34%) LA
 1016 (3.34%) RA
 45 (0.15%) LA & RA
CTCF(+) RAD21(+)  9447 (31.02%) LA
 9462 (31.07%) RA
 3673 (12.06%) LA + RA
CTCF directionality
(30535 cases)		  3360 (11%)Convergent ≫ ≪
 100 (0.33%)Divergent ≪ ≫
 1374 (4.5%)Tandem ≫ ≫
 12332 (40.39%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF4834202.6870.650
ZBTB24069156.4000.632
Sox5492870.0910.560
ZNF354C622068.6920.480
FOXL1322847.7330.527
FOXP3308745.3840.524
FOXI1307044.7190.530
FOXO4307044.7190.527
FOXO6307044.7190.526
LHX5315344.1230.513
 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