Information
Accession GMS-64-17 (FID: 578)Browse (ALL)
Title Hi-C on HAP-1 +/- WAPL or SCC4 KO
HiC file 4DNFIK61ILGM (3.46 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 (278.55 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 5935 domains
10438 boundaries
GMS Loop 7791 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (10438)
CTCF(+) RAD21(-)  276 (2.64%)
CTCF(-) RAD21(+)  328 (3.14%)
CTCF(+) RAD21(+)  1421 (13.61%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB2 312 24.543 0.543
CTCF 311 24.367 0.544
RHOXF1 396 15.409 0.519
Sox5 593 12.436 0.545
ZNF518A 568 10.199 0.526
HOXB6 378 9.070 0.512
NFATC2 227 8.762 0.543
MEIS1 458 8.644 0.515
VAX1 305 8.043 0.509
Nr2e3 352 7.843 0.512
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (7791 x2 anchors)
CTCF(+) RAD21(-)  276 (3.54%) LA
 318 (4.08%) RA
 15 (0.19%) LA & RA
CTCF(-) RAD21(+)  263 (3.38%) LA
 213 (2.73%) RA
 8 (0.1%) LA & RA
CTCF(+) RAD21(+)  1731 (22.22%) LA
 1763 (22.63%) RA
 571 (7.33%) LA + RA
CTCF directionality
(7792 cases)		  457 (5.86%)Convergent ≫ ≪
 21 (0.27%)Divergent ≪ ≫
 254 (3.26%)Tandem ≫ ≫
 2626 (33.7%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF89596.9220.587
ZBTB271065.1710.579
FOXP377629.4930.524
FOXI177329.1640.528
FOXO477329.1640.523
FOXO677329.1640.526
NFATC249628.1110.562
Arid3a61526.6060.530
RHOXF162725.3280.505
Dlx247122.7650.507
 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