Information
Accession GMS-64-50 (FID: 620)Browse (ALL)
Title in situ Hi-C on primary human cardiomyocytes
HiC file 4DNFIIOMQOKT (6.01 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-08 12:49:07
Last update date2025-02-08 12:49:07
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 2025-02-08 12:49:07
Reference hg38 (Human)  
Result file DomainCall.tar.gz (319.54 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 6269 domains
11312 boundaries
GMS Loop 12761 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (11312)
CTCF(+) RAD21(-)  406 (3.59%)
CTCF(-) RAD21(+)  325 (2.87%)
CTCF(+) RAD21(+)  1480 (13.08%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 327 23.459 0.545
ZBTB2 286 17.028 0.540
GATA3 495 12.418 0.509
RHOXF1 381 9.107 0.515
MEIS1 489 8.777 0.520
NR1I3 437 8.631 0.505
FOXL1 422 7.487 0.523
Arid3a 300 7.319 0.523
HOXA1 360 6.845 0.506
FOXO4 404 6.600 0.529
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (12761 x2 anchors)
CTCF(+) RAD21(-)  523 (4.1%) LA
 559 (4.38%) RA
 30 (0.24%) LA & RA
CTCF(-) RAD21(+)  413 (3.24%) LA
 411 (3.22%) RA
 16 (0.13%) LA & RA
CTCF(+) RAD21(+)  3312 (25.95%) LA
 3333 (26.12%) RA
 1112 (8.71%) LA + RA
CTCF directionality
(12774 cases)		  982 (7.69%)Convergent ≫ ≪
 60 (0.47%)Divergent ≪ ≫
 423 (3.31%)Tandem ≫ ≫
 4823 (37.76%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF1500113.1310.611
ZBTB2136396.6580.599
Sox5228265.1040.577
Arid3a117951.2850.524
FOXL1146044.9400.524
FOXI1139441.7090.539
FOXO4139441.7090.532
FOXO6139441.7090.537
FOXP3139441.7090.531
NFATC296138.7130.578
 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