Information
Accession GMS-64-17 (FID: 579)Browse (ALL)
Title Hi-C on HAP-1 +/- WAPL or SCC4 KO
HiC file 4DNFIO6M7YK8 (3.48 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-31 10:15:47
Last update date2025-01-31 10:15:47
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 2025-01-31 10:15:48
Reference hg38 (Human)  
Result file DomainCall.tar.gz (280.96 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 5973 domains
10521 boundaries
GMS Loop 7636 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (10521)
CTCF(+) RAD21(-)  362 (3.44%)
CTCF(-) RAD21(+)  356 (3.38%)
CTCF(+) RAD21(+)  1436 (13.65%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 310 23.836 0.548
ZBTB2 275 17.985 0.543
MEIS1 810 10.979 0.508
Sox5 568 10.285 0.542
Foxj2 265 9.675 0.508
Nr2e3 354 8.167 0.503
FOXN3 334 8.037 0.518
FOXO3 351 7.884 0.511
FOXL1 367 6.754 0.518
HOXB5 284 6.442 0.514
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (7636 x2 anchors)
CTCF(+) RAD21(-)  265 (3.47%) LA
 262 (3.43%) RA
 7 (0.09%) LA & RA
CTCF(-) RAD21(+)  261 (3.42%) LA
 221 (2.89%) RA
 8 (0.1%) LA & RA
CTCF(+) RAD21(+)  1569 (20.55%) LA
 1617 (21.18%) RA
 452 (5.92%) LA + RA
CTCF directionality
(7637 cases)		  404 (5.29%)Convergent ≫ ≪
 11 (0.14%)Divergent ≪ ≫
 168 (2.2%)Tandem ≫ ≫
 2549 (33.38%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF77778.6160.584
ZBTB273170.7100.574
ZNF354C143049.1490.476
Sox5113845.7950.566
Nr2e371234.8980.522
MEIS184933.2630.531
FOXL176531.3200.523
FOXI173129.9960.528
FOXO473029.8810.525
FOXO673029.8810.525
 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