Information
Accession GMS-64-52 (FID: 625)Browse (ALL)
Title in situ Hi-C on primary human cardiomyocytes
HiC file 4DNFIGU793GK (10.36 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-08 13:02:05
Last update date2025-02-08 13:02:05
Contact Sung-Joon PARK
park AT hgc.jp
The University of Tokyo
Sharingopen access
Keywords Hi-C  4DN  contact matrix 
 Domain/Loop Calling Information

URL copied to the clipboard
Submit date 2025-02-08 13:02:09
Reference hg38 (Human)  
Result file DomainCall.tar.gz (322.97 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 6801 domains
12032 boundaries
GMS Loop 12236 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (12032)
CTCF(+) RAD21(-)  411 (3.42%)
CTCF(-) RAD21(+)  455 (3.78%)
CTCF(+) RAD21(+)  1729 (14.37%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5 776 21.195 0.555
CTCF 329 21.083 0.537
RHOXF1 466 17.600 0.519
ZBTB2 300 16.820 0.542
NFATC2 316 14.577 0.550
HOXC4 310 14.258 0.505
HOXD4 328 13.888 0.509
HOXB4 325 13.519 0.509
HOXB1 425 12.316 0.514
Nr2e3 457 11.875 0.506
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (12236 x2 anchors)
CTCF(+) RAD21(-)  496 (4.05%) LA
 508 (4.15%) RA
 33 (0.27%) LA & RA
CTCF(-) RAD21(+)  378 (3.09%) LA
 379 (3.1%) RA
 20 (0.16%) LA & RA
CTCF(+) RAD21(+)  3027 (24.74%) LA
 3043 (24.87%) RA
 975 (7.97%) LA + RA
CTCF directionality
(12244 cases)		  872 (7.12%)Convergent ≫ ≪
 50 (0.41%)Divergent ≪ ≫
 379 (3.1%)Tandem ≫ ≫
 4488 (36.65%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF1461115.0560.604
ZBTB2122585.8970.593
Sox5223785.5820.581
ZNF354C151558.5030.517
MEIS1277457.2350.534
RHOXF1138654.7470.519
FOXL1145353.1300.529
FOXO4137550.5220.525
FOXP3138250.4680.519
FOXI1137650.2670.535
 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