Information
Accession GMS-64-50 (FID: 621)Browse (ALL)
Title in situ Hi-C on primary human cardiomyocytes
HiC file 4DNFISDI5IAS (6.48 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 (318.26 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 6014 domains
10826 boundaries
GMS Loop 13005 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (10826)
CTCF(+) RAD21(-)  353 (3.26%)
CTCF(-) RAD21(+)  373 (3.45%)
CTCF(+) RAD21(+)  1408 (13.01%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5 678 17.131 0.562
ZBTB2 272 16.485 0.538
CTCF 269 16.029 0.540
FOXI1 418 14.038 0.528
FOXO4 418 14.038 0.527
FOXO6 418 14.038 0.527
FOXP3 418 14.038 0.523
FOXL1 435 13.501 0.521
HOXD4 276 12.460 0.509
HOXB4 275 12.329 0.508
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (13005 x2 anchors)
CTCF(+) RAD21(-)  594 (4.57%) LA
 589 (4.53%) RA
 36 (0.28%) LA & RA
CTCF(-) RAD21(+)  390 (3%) LA
 418 (3.21%) RA
 18 (0.14%) LA & RA
CTCF(+) RAD21(+)  3379 (25.98%) LA
 3327 (25.58%) RA
 1125 (8.65%) LA + RA
CTCF directionality
(13012 cases)		  1008 (7.75%)Convergent ≫ ≪
 60 (0.46%)Divergent ≪ ≫
 430 (3.3%)Tandem ≫ ≫
 4907 (37.71%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF1415100.0550.608
Sox5232374.0010.576
ZNF354C156271.0410.441
ZBTB2109263.6550.595
Arid3a123762.3990.571
FOXL1153957.3420.531
MEIS1167555.1530.497
FOXO4147053.0340.535
FOXP3147053.0340.530
FOXI1147052.6770.537
 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