Information
Accession GMS-64-67 (FID: 651)Browse (ALL)
Title Hi-C on WTC-11 cardiac differention timecourse
HiC file 4DNFIXF2GL4C (5.76 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-18 15:16:04
Last update date2025-02-18 15:16:04
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 15:16:04
Reference hg38 (Human)  
Result file DomainCall.tar.gz (431.45 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 9995 domains
17158 boundaries
GMS Loop 29996 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (17158)
CTCF(+) RAD21(-)  602 (3.51%)
CTCF(-) RAD21(+)  488 (2.84%)
CTCF(+) RAD21(+)  2402 (14%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 525 30.536 0.551
ZBTB2 500 27.392 0.543
HOXB1 566 13.408 0.511
HOXB6 603 12.221 0.519
NKX6-1 632 11.581 0.512
Sox5 918 11.241 0.541
VSX1 633 10.118 0.519
Arid3a 429 9.840 0.523
LHX5 336 9.601 0.514
VSX2 373 9.179 0.517
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (29996 x2 anchors)
CTCF(+) RAD21(-)  1490 (4.97%) LA
 1462 (4.87%) RA
 68 (0.23%) LA & RA
CTCF(-) RAD21(+)  908 (3.03%) LA
 893 (2.98%) RA
 37 (0.12%) LA & RA
CTCF(+) RAD21(+)  8488 (28.3%) LA
 8560 (28.54%) RA
 2980 (9.93%) LA + RA
CTCF directionality
(30051 cases)		  2730 (9.08%)Convergent ≫ ≪
 126 (0.42%)Divergent ≪ ≫
 1226 (4.08%)Tandem ≫ ≫
 11946 (39.75%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF4636194.6200.645
ZBTB23885148.8620.625
Sox5402937.5180.553
FOXP3249027.7110.524
FOXL1260527.6780.526
FOXO4248227.4350.526
FOXO6248227.4350.526
FOXI1248127.4010.528
RHOXF1223027.1410.511
MEIS1280825.5640.515
 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