Information
Accession GMS-64-71 (FID: 657)Browse (ALL)
Title in situ Hi-C on primary human cardiomyocytes
HiC file 4DNFIFUBA8FE (6.90 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-18 15:18:39
Last update date2025-02-18 15:18:39
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 15:18:39
Reference hg38 (Human)  
Result file DomainCall.tar.gz (313.35 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 6200 domains
11111 boundaries
GMS Loop 11457 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (11111)
CTCF(+) RAD21(-)  401 (3.61%)
CTCF(-) RAD21(+)  297 (2.67%)
CTCF(+) RAD21(+)  1529 (13.76%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
MEIS1 547 25.260 0.517
CTCF 308 21.145 0.535
Sox5 725 20.812 0.558
ZBTB2 294 18.922 0.538
FOXL1 481 17.425 0.528
FOXI1 450 15.038 0.532
FOXO4 450 15.038 0.531
FOXO6 450 15.038 0.531
FOXP3 450 15.038 0.528
HOXB4 310 14.848 0.515
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (11457 x2 anchors)
CTCF(+) RAD21(-)  396 (3.46%) LA
 431 (3.76%) RA
 20 (0.17%) LA & RA
CTCF(-) RAD21(+)  411 (3.59%) LA
 422 (3.68%) RA
 24 (0.21%) LA & RA
CTCF(+) RAD21(+)  2794 (24.39%) LA
 2789 (24.34%) RA
 865 (7.55%) LA + RA
CTCF directionality
(11463 cases)		  757 (6.6%)Convergent ≫ ≪
 34 (0.3%)Divergent ≪ ≫
 328 (2.86%)Tandem ≫ ≫
 4184 (36.5%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF1284102.3710.598
ZBTB2121693.5240.590
Sox5219191.8460.582
FOXL1146866.6940.525
FOXP3139764.7740.537
FOXI1139064.0430.543
FOXO4139064.0430.533
FOXO6139064.0430.541
MEIS1154457.0240.512
NKX6-1123241.9700.503
 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