Information
Accession GMS-64-69 (FID: 653)Browse (ALL)
Title in situ Hi-C on primary human cardiomyocytes
HiC file 4DNFIYU853WO (5.97 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-18 15:16:30
Last update date2025-02-18 15:16:30
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 15:16:31
Reference hg38 (Human)  
Result file DomainCall.tar.gz (294.57 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 5255 domains
9599 boundaries
GMS Loop 9818 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (9599)
CTCF(+) RAD21(-)  327 (3.41%)
CTCF(-) RAD21(+)  272 (2.83%)
CTCF(+) RAD21(+)  1269 (13.22%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5 603 22.022 0.559
ZBTB2 266 19.949 0.546
CTCF 259 18.724 0.541
ZNF518A 558 11.169 0.521
FOXL1 380 11.168 0.521
MEIS1 406 10.632 0.491
FOXI1 363 10.392 0.523
FOXO4 363 10.392 0.522
FOXO6 363 10.392 0.521
FOXP3 363 10.392 0.518
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (9818 x2 anchors)
CTCF(+) RAD21(-)  436 (4.44%) LA
 444 (4.52%) RA
 20 (0.2%) LA & RA
CTCF(-) RAD21(+)  291 (2.96%) LA
 309 (3.15%) RA
 20 (0.2%) LA & RA
CTCF(+) RAD21(+)  2328 (23.71%) LA
 2390 (24.34%) RA
 753 (7.67%) LA + RA
CTCF directionality
(9823 cases)		  638 (6.49%)Convergent ≫ ≪
 41 (0.42%)Divergent ≪ ≫
 321 (3.27%)Tandem ≫ ≫
 3608 (36.73%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF1151106.4010.594
ZBTB298481.8970.579
Sox5176575.9310.579
MEIS1127947.4530.517
Nr2e3105245.9250.519
FOXL1115943.0260.528
RHOXF1108941.9010.522
FOXP3110939.2200.526
FOXI1110238.5350.535
FOXO4110238.5350.532
 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