Information
Accession GMS-64-72 (FID: 659)Browse (ALL)
Title Hi-C on WTC-11 cardiac differention timecourse
HiC file 4DNFIIMDXANO (6.03 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-18 15:23:04
Last update date2025-02-18 15:23:04
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 15:23:04
Reference hg38 (Human)  
Result file DomainCall.tar.gz (452.32 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 10385 domains
17796 boundaries
GMS Loop 32306 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (17796)
CTCF(+) RAD21(-)  579 (3.25%)
CTCF(-) RAD21(+)  538 (3.02%)
CTCF(+) RAD21(+)  2523 (14.18%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 638 42.982 0.545
ZBTB2 592 36.888 0.540
Sox5 1010 16.993 0.545
HOXB6 597 7.972 0.512
HOXB1 553 7.820 0.504
HOXA1 464 7.652 0.508
Nr2e3 569 7.200 0.512
SOX18 586 7.184 0.499
HOXB5 396 7.001 0.510
FOXL1 610 6.960 0.512
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (32306 x2 anchors)
CTCF(+) RAD21(-)  1351 (4.18%) LA
 1298 (4.02%) RA
 67 (0.21%) LA & RA
CTCF(-) RAD21(+)  1230 (3.81%) LA
 1149 (3.56%) RA
 50 (0.15%) LA & RA
CTCF(+) RAD21(+)  9190 (28.45%) LA
 9266 (28.68%) RA
 3248 (10.05%) LA + RA
CTCF directionality
(32374 cases)		  2865 (8.85%)Convergent ≫ ≪
 109 (0.34%)Divergent ≪ ≫
 1273 (3.93%)Tandem ≫ ≫
 12747 (39.37%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF5487224.9710.641
ZBTB24723180.3470.620
Sox5423435.9580.550
FOXL1279926.3250.529
VSX1279424.8460.513
FOXI1266624.6660.535
FOXO4266624.6660.532
FOXO6266624.6660.532
FOXP3266624.6660.529
MEIS1296122.2600.515
 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