Information
Accession GMS-64-18 (FID: 580)Browse (ALL)
Title Hi-C on HAP-1 +/- WAPL or SCC4 KO
HiC file 4DNFIYD8LO9Z (3.37 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-31 10:26:19
Last update date2025-01-31 10:26:19
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 10:26:21
Reference hg38 (Human)  
Result file DomainCall.tar.gz (313.25 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 6716 domains
11661 boundaries
GMS Loop 11706 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (11661)
CTCF(+) RAD21(-)  401 (3.44%)
CTCF(-) RAD21(+)  337 (2.89%)
CTCF(+) RAD21(+)  1741 (14.93%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 429 39.636 0.547
ZBTB2 370 29.174 0.544
Sox5 682 12.820 0.549
RHOXF1 424 12.796 0.522
FOXL1 443 10.713 0.519
VAX1 349 10.445 0.513
FOXO4 415 9.348 0.519
FOXO6 415 9.348 0.519
FOXP3 415 9.348 0.516
FOXI1 415 9.213 0.521
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (11706 x2 anchors)
CTCF(+) RAD21(-)  463 (3.96%) LA
 444 (3.79%) RA
 18 (0.15%) LA & RA
CTCF(-) RAD21(+)  371 (3.17%) LA
 370 (3.16%) RA
 13 (0.11%) LA & RA
CTCF(+) RAD21(+)  2613 (22.32%) LA
 2625 (22.42%) RA
 785 (6.71%) LA + RA
CTCF directionality
(11712 cases)		  637 (5.44%)Convergent ≫ ≪
 47 (0.4%)Divergent ≪ ≫
 360 (3.07%)Tandem ≫ ≫
 4069 (34.74%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF1512129.1880.593
ZBTB2119688.1040.582
Sox5174246.5590.555
Arid3a84531.3100.525
MEIS1123229.6680.519
FOXL1115527.0470.526
ZNF354C102026.4910.482
FOXI1110326.3110.524
FOXO4110326.3110.522
FOXO6110326.3110.522
 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