Information
Accession GMS-64-26 (FID: 591)Browse (ALL)
Title Hi-C on HCT116
HiC file 4DNFIHSUIRFY (2.84 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-04 14:00:15
Last update date2025-02-04 14:00:15
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 2025-02-04 14:00:16
Reference hg38 (Human)  
Result file DomainCall.tar.gz (274.60 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3446 domains
6194 boundaries
GMS Loop 11491 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (6194)
CTCF(+) RAD21(-)  213 (3.44%)
CTCF(-) RAD21(+)  180 (2.91%)
CTCF(+) RAD21(+)  939 (15.16%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 251 36.609 0.556
ZBTB2 229 30.563 0.548
FOXN3 233 8.846 0.544
VSX1 125 6.764 0.515
MEIS1 272 6.567 0.513
Nr2e3 224 6.424 0.522
FOXO4 208 6.276 0.529
FOXO6 208 6.276 0.528
FOXP3 208 6.276 0.526
FOXL1 218 6.262 0.529
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (11491 x2 anchors)
CTCF(+) RAD21(-)  464 (4.04%) LA
 520 (4.53%) RA
 29 (0.25%) LA & RA
CTCF(-) RAD21(+)  356 (3.1%) LA
 388 (3.38%) RA
 9 (0.08%) LA & RA
CTCF(+) RAD21(+)  2511 (21.85%) LA
 2463 (21.43%) RA
 608 (5.29%) LA + RA
CTCF directionality
(11492 cases)		  430 (3.74%)Convergent ≫ ≪
 78 (0.68%)Divergent ≪ ≫
 362 (3.15%)Tandem ≫ ≫
 4220 (36.72%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB2104171.1670.570
CTCF103770.6800.588
FOXL1127046.1010.530
FOXP3121243.6540.531
FOXI1120543.3320.536
FOXO4120543.3320.534
FOXO6120543.3320.534
MEIS1138143.0930.528
ZNF354C115542.2860.498
Nr2e3117237.2690.511
 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