Information
Accession GMS-64-29 (FID: 596)Browse (ALL)
Title Hi-C on HCT116
HiC file 4DNFIXTAS6EE (3.42 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-04 14:08:03
Last update date2025-02-04 14:08:03
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 14:08:03
Reference hg38 (Human)  
Result file DomainCall.tar.gz (260.85 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 4673 domains
8454 boundaries
GMS Loop 6334 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (8454)
CTCF(+) RAD21(-)  277 (3.28%)
CTCF(-) RAD21(+)  276 (3.26%)
CTCF(+) RAD21(+)  1184 (14.01%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 263 24.591 0.547
ZBTB2 215 15.351 0.544
HOXB6 319 11.517 0.511
MEIS1 366 10.394 0.515
HOXB1 295 9.644 0.513
FOXL1 310 7.897 0.515
PRRX1 290 7.469 0.506
PRRX2 283 7.405 0.509
LHX9 280 7.313 0.509
FOXP3 300 7.294 0.520
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (6334 x2 anchors)
CTCF(+) RAD21(-)  228 (3.6%) LA
 247 (3.9%) RA
 12 (0.19%) LA & RA
CTCF(-) RAD21(+)  226 (3.57%) LA
 219 (3.46%) RA
 13 (0.21%) LA & RA
CTCF(+) RAD21(+)  1216 (19.2%) LA
 1280 (20.21%) RA
 298 (4.7%) LA + RA
CTCF directionality
(6337 cases)		  258 (4.07%)Convergent ≫ ≪
 16 (0.25%)Divergent ≪ ≫
 142 (2.24%)Tandem ≫ ≫
 2145 (33.85%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF57460.5060.575
ZBTB250247.1620.562
Sox597340.2950.578
Nr2e3102625.6850.514
RHOXF153525.4250.512
FOXL163724.8640.528
FOXP361624.5000.527
FOXI161524.3800.533
FOXO461524.3800.531
FOXO661524.3800.531
 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