Information
Accession GMS-64-79 (FID: 669)Browse (ALL)
Title in situ Hi-C on an allelic series of iPSCs differentiated to cardiac cells
HiC file 4DNFIESB8H1S (8.79 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-18 15:32:13
Last update date2025-02-18 15:32:13
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 15:32:13
Reference hg38 (Human)  
Result file DomainCall.tar.gz (453.64 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 10701 domains
18074 boundaries
GMS Loop 32240 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (18074)
CTCF(+) RAD21(-)  667 (3.69%)
CTCF(-) RAD21(+)  551 (3.05%)
CTCF(+) RAD21(+)  2710 (14.99%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 514 26.293 0.555
Sox5 1140 25.377 0.551
MEIS1 864 18.352 0.509
Nr2e3 709 17.287 0.515
SHOX 428 16.779 0.510
ZBTB2 420 15.961 0.544
NFATC2 465 14.009 0.541
RAX2 441 13.918 0.510
Shox2 399 12.884 0.510
RHOXF1 585 12.731 0.515
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (32240 x2 anchors)
CTCF(+) RAD21(-)  1448 (4.49%) LA
 1490 (4.62%) RA
 96 (0.3%) LA & RA
CTCF(-) RAD21(+)  1084 (3.36%) LA
 1028 (3.19%) RA
 42 (0.13%) LA & RA
CTCF(+) RAD21(+)  9382 (29.1%) LA
 9403 (29.17%) RA
 3519 (10.92%) LA + RA
CTCF directionality
(32313 cases)		  3100 (9.59%)Convergent ≫ ≪
 134 (0.41%)Divergent ≪ ≫
 1418 (4.39%)Tandem ≫ ≫
 12565 (38.89%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF5284213.5620.646
ZBTB24342159.1850.626
Sox5516471.7400.560
FOXL1342150.7300.535
FOXO4322947.4640.533
FOXP3322947.4640.529
FOXO6323247.2110.532
FOXI1323047.1350.535
LHX5329747.1210.512
MEIS1354646.1730.506
 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