Information
Accession GMS-64-81 (FID: 672)Browse (ALL)
Title in situ Hi-C on an allelic series of iPSCs differentiated to cardiac cells
HiC file 4DNFIK3NAVTO (8.55 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-18 15:41:00
Last update date2025-02-18 15:41:00
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 15:41:00
Reference hg38 (Human)  
Result file DomainCall.tar.gz (461.77 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 11180 domains
18771 boundaries
GMS Loop 31378 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (18771)
CTCF(+) RAD21(-)  682 (3.63%)
CTCF(-) RAD21(+)  495 (2.64%)
CTCF(+) RAD21(+)  2739 (14.59%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 631 38.245 0.553
ZBTB2 601 34.524 0.543
Sox5 1116 18.961 0.542
Arid3a 567 17.172 0.513
MEIS1 873 16.736 0.508
ZNF354C 708 16.017 0.460
RHOXF1 672 15.755 0.510
Nr2e3 692 13.480 0.512
PRRX2 676 13.025 0.511
NFATC2 461 12.931 0.520
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (31378 x2 anchors)
CTCF(+) RAD21(-)  1466 (4.67%) LA
 1449 (4.62%) RA
 104 (0.33%) LA & RA
CTCF(-) RAD21(+)  1004 (3.2%) LA
 961 (3.06%) RA
 43 (0.14%) LA & RA
CTCF(+) RAD21(+)  8817 (28.1%) LA
 8931 (28.46%) RA
 3327 (10.6%) LA + RA
CTCF directionality
(31445 cases)		  2955 (9.4%)Convergent ≫ ≪
 137 (0.44%)Divergent ≪ ≫
 1346 (4.28%)Tandem ≫ ≫
 11921 (37.91%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF4231159.0890.637
ZBTB23754131.9550.617
Sox5497157.5270.559
FOXL1325544.8640.536
FOXP3312942.8990.526
FOXI1311042.1910.529
FOXO4311042.1910.524
FOXO6311042.1910.525
MEIS1357342.0190.517
NKX6-1306538.2310.511
 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