Information
Accession GMS-64-18 (FID: 581)Browse (ALL)
Title Hi-C on HAP-1 +/- WAPL or SCC4 KO
HiC file 4DNFI1CJV7RG (3.38 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 (310.38 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 6691 domains
11670 boundaries
GMS Loop 11582 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (11670)
CTCF(+) RAD21(-)  418 (3.58%)
CTCF(-) RAD21(+)  288 (2.47%)
CTCF(+) RAD21(+)  1714 (14.69%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 375 29.987 0.551
ZBTB2 311 19.607 0.545
RHOXF1 386 13.625 0.516
NFATC2 286 10.628 0.545
NKX6-1 425 9.833 0.505
HOXB6 424 9.468 0.513
Nobox 287 8.966 0.511
Sox5 672 8.798 0.550
MEIS1 380 8.426 0.495
VAX1 361 8.314 0.513
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (11582 x2 anchors)
CTCF(+) RAD21(-)  466 (4.02%) LA
 461 (3.98%) RA
 25 (0.22%) LA & RA
CTCF(-) RAD21(+)  359 (3.1%) LA
 371 (3.2%) RA
 15 (0.13%) LA & RA
CTCF(+) RAD21(+)  2584 (22.31%) LA
 2580 (22.28%) RA
 757 (6.54%) LA + RA
CTCF directionality
(11587 cases)		  629 (5.43%)Convergent ≫ ≪
 51 (0.44%)Divergent ≪ ≫
 340 (2.93%)Tandem ≫ ≫
 4061 (35.05%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB21304103.3890.587
CTCF124095.1170.591
Sox5171834.3810.552
FOXL1112430.3170.530
Arid3a80029.2380.583
FOXI1107428.6910.534
FOXO4107428.6910.533
FOXO6107428.6910.533
FOXP3107428.6910.531
MEIS1206423.7980.505
 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