Information
Accession GMS-64-71 (FID: 658)Browse (ALL)
Title in situ Hi-C on primary human cardiomyocytes
HiC file 4DNFIM351CAA (7.56 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 (325.51 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 6522 domains
11628 boundaries
GMS Loop 12353 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (11628)
CTCF(+) RAD21(-)  442 (3.8%)
CTCF(-) RAD21(+)  336 (2.89%)
CTCF(+) RAD21(+)  1606 (13.81%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5 754 23.345 0.566
ZBTB2 327 22.241 0.537
CTCF 301 18.241 0.535
RHOXF1 449 16.821 0.513
MEIS1 542 15.282 0.508
Nr2e3 458 14.918 0.511
ZNF354C 495 12.374 0.495
HOXB5 385 12.062 0.511
FOXL1 473 11.985 0.518
Nobox 336 11.694 0.505
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (12353 x2 anchors)
CTCF(+) RAD21(-)  522 (4.23%) LA
 556 (4.5%) RA
 38 (0.31%) LA & RA
CTCF(-) RAD21(+)  411 (3.33%) LA
 433 (3.51%) RA
 22 (0.18%) LA & RA
CTCF(+) RAD21(+)  3131 (25.35%) LA
 3131 (25.35%) RA
 1025 (8.3%) LA + RA
CTCF directionality
(12363 cases)		  887 (7.17%)Convergent ≫ ≪
 52 (0.42%)Divergent ≪ ≫
 428 (3.46%)Tandem ≫ ≫
 4626 (37.42%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF1543123.8860.603
ZBTB21489117.0440.592
Sox5238196.0620.581
Arid3a120665.4940.586
FOXL1156564.5880.537
FOXI1147858.9390.541
FOXO4147858.9390.531
FOXO6147858.9390.537
FOXP3147858.9390.532
NFATC297249.6090.581
 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