Information
Accession GMS-64-51 (FID: 623)Browse (ALL)
Title in situ Hi-C on primary human cardiomyocytes
HiC file 4DNFI5TI7AOU (6.60 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-08 12:49:26
Last update date2025-02-08 12:49:26
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 12:49:26
Reference hg38 (Human)  
Result file DomainCall.tar.gz (315.53 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 6303 domains
11280 boundaries
GMS Loop 11634 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (11280)
CTCF(+) RAD21(-)  444 (3.94%)
CTCF(-) RAD21(+)  359 (3.18%)
CTCF(+) RAD21(+)  1591 (14.1%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C 477 18.423 0.476
CTCF 276 15.654 0.545
Arid3a 359 15.194 0.578
ZBTB2 272 15.075 0.541
FOXI1 432 14.387 0.525
FOXO6 432 14.387 0.522
FOXO4 431 14.273 0.522
FOXP3 431 14.273 0.519
FOXL1 263 12.002 0.515
HOXB4 298 11.763 0.505
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (11634 x2 anchors)
CTCF(+) RAD21(-)  466 (4.01%) LA
 483 (4.15%) RA
 25 (0.21%) LA & RA
CTCF(-) RAD21(+)  343 (2.95%) LA
 390 (3.35%) RA
 20 (0.17%) LA & RA
CTCF(+) RAD21(+)  2862 (24.6%) LA
 2880 (24.76%) RA
 882 (7.58%) LA + RA
CTCF directionality
(11644 cases)		  813 (6.98%)Convergent ≫ ≪
 42 (0.36%)Divergent ≪ ≫
 327 (2.81%)Tandem ≫ ≫
 4347 (37.33%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF1591141.0250.604
ZBTB2116484.8950.592
Sox5211878.8250.575
MEIS1150059.6930.519
ZNF518A181652.4250.526
FOXL1138049.3530.540
FOXO6131347.7630.534
FOXI1131247.6710.537
FOXO4131247.6710.534
FOXP3131247.6710.529
 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