Information
Accession GMS-64-76 (FID: 664)Browse (ALL)
Title in situ Hi-C on an allelic series of iPSCs differentiated to cardiac cells
HiC file 4DNFIB7KBAH5 (9.20 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-18 15:29:25
Last update date2025-02-18 15:29:25
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 15:29:26
Reference hg38 (Human)  
Result file DomainCall.tar.gz (432.52 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 10949 domains
18364 boundaries
GMS Loop 27628 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (18364)
CTCF(+) RAD21(-)  576 (3.14%)
CTCF(-) RAD21(+)  560 (3.05%)
CTCF(+) RAD21(+)  2574 (14.02%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB2 611 37.218 0.545
CTCF 575 32.718 0.550
MEIS1 857 26.020 0.509
Sox5 1110 21.728 0.545
Nr2e3 675 16.488 0.514
RHOXF1 685 16.293 0.513
HOXD4 466 14.191 0.512
HOXB4 465 14.100 0.511
HOXC4 431 13.855 0.507
FOXL1 692 13.097 0.519
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (27628 x2 anchors)
CTCF(+) RAD21(-)  1267 (4.59%) LA
 1259 (4.56%) RA
 71 (0.26%) LA & RA
CTCF(-) RAD21(+)  902 (3.26%) LA
 863 (3.12%) RA
 34 (0.12%) LA & RA
CTCF(+) RAD21(+)  7520 (27.22%) LA
 7647 (27.68%) RA
 2718 (9.84%) LA + RA
CTCF directionality
(27689 cases)		  2489 (8.99%)Convergent ≫ ≪
 99 (0.36%)Divergent ≪ ≫
 1073 (3.88%)Tandem ≫ ≫
 10493 (37.9%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF4446204.9170.633
ZBTB23561146.5410.617
Sox5447164.6120.566
FOXL1292345.5910.531
ZNF354C272744.5520.526
FOXI1277942.2650.536
FOXO4277942.2650.533
FOXO6277942.2650.533
FOXP3277942.2650.529
RHOXF1243037.1660.509
 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