Information
Accession GMS-64-20 (FID: 584)Browse (ALL)
Title Hi-C on HAP-1 +/- WAPL or SCC4 KO
HiC file 4DNFIRQF7JOU (3.84 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-31 10:44:58
Last update date2025-01-31 10:44:58
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 10:44:58
Reference hg38 (Human)  
Result file DomainCall.tar.gz (250.91 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 4128 domains
7520 boundaries
GMS Loop 5460 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (7520)
CTCF(+) RAD21(-)  270 (3.59%)
CTCF(-) RAD21(+)  193 (2.57%)
CTCF(+) RAD21(+)  865 (11.5%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 166 10.028 0.528
TEAD3 171 7.504 0.493
ZBTB2 143 6.440 0.536
MEIS1 305 5.495 0.504
ISL2 180 5.463 0.523
Smad4 201 5.367 0.488
NFATC2 176 5.221 0.541
HOXC4 167 5.177 0.507
NRF1 132 4.943 0.525
RHOXF1 241 4.832 0.518
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (5460 x2 anchors)
CTCF(+) RAD21(-)  183 (3.35%) LA
 212 (3.88%) RA
 7 (0.13%) LA & RA
CTCF(-) RAD21(+)  168 (3.08%) LA
 133 (2.44%) RA
 3 (0.05%) LA & RA
CTCF(+) RAD21(+)  1069 (19.58%) LA
 1073 (19.65%) RA
 299 (5.48%) LA + RA
CTCF directionality
(5461 cases)		  272 (4.98%)Convergent ≫ ≪
 25 (0.46%)Divergent ≪ ≫
 97 (1.78%)Tandem ≫ ≫
 1751 (32.06%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF59980.2000.572
ZBTB245449.0340.571
Sox572522.0470.550
FOXL149521.8810.520
MEIS155121.5570.516
FOXI146819.9640.524
FOXO446819.9640.520
FOXO646819.9640.523
FOXP346819.9640.520
Nr2e347518.5090.523
 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