Information
Accession GMS-64-73 (FID: 660)Browse (ALL)
Title Hi-C on WTC-11 cardiac differention timecourse
HiC file 4DNFIF78U26G (4.66 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-18 15:23:06
Last update date2025-02-18 15:23:06
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 15:23:06
Reference hg38 (Human)  
Result file DomainCall.tar.gz (393.68 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 8242 domains
14399 boundaries
GMS Loop 24907 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (14399)
CTCF(+) RAD21(-)  524 (3.64%)
CTCF(-) RAD21(+)  413 (2.87%)
CTCF(+) RAD21(+)  2048 (14.22%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 444 29.458 0.543
ZBTB2 373 19.677 0.537
Sox5 793 17.053 0.548
MEIS1 440 8.965 0.511
RHOXF1 404 7.281 0.511
TEAD3 264 7.177 0.504
NFAT5 377 7.010 0.508
CTCFL 252 6.270 0.534
GATA3 540 6.197 0.511
HOXB1 482 6.106 0.510
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (24907 x2 anchors)
CTCF(+) RAD21(-)  1047 (4.2%) LA
 1054 (4.23%) RA
 47 (0.19%) LA & RA
CTCF(-) RAD21(+)  851 (3.42%) LA
 873 (3.51%) RA
 36 (0.14%) LA & RA
CTCF(+) RAD21(+)  6935 (27.84%) LA
 6997 (28.09%) RA
 2517 (10.11%) LA + RA
CTCF directionality
(24971 cases)		  2275 (9.11%)Convergent ≫ ≪
 94 (0.38%)Divergent ≪ ≫
 925 (3.7%)Tandem ≫ ≫
 9573 (38.34%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF3929196.8260.635
ZBTB23399158.2900.619
Sox5352550.9330.555
FOXL1227630.7870.524
Nr2e3201729.9470.513
FOXI1217628.6750.530
FOXO4217628.6750.525
FOXO6217628.6750.524
FOXP3217628.6750.522
Arid3a164227.4150.556
 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