Information
Accession GMS-64-25 (FID: 590)Browse (ALL)
Title Hi-C on RAD21-AID tagged HCT-116
HiC file 4DNFIV56OFE3 (5.96 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-04 13:59:23
Last update date2025-02-04 13:59:23
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 13:59:23
Reference hg38 (Human)  
Result file DomainCall.tar.gz (188.99 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 872 domains
1657 boundaries
GMS Loop 1390 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (1657)
CTCF(+) RAD21(-)  44 (2.66%)
CTCF(-) RAD21(+)  48 (2.9%)
CTCF(+) RAD21(+)  155 (9.35%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
RHOXF1 71 8.843 0.502
ZNF518A 110 6.449 0.523
HOXC4 48 5.963 0.506
Foxj2 55 5.518 0.502
VAX1 59 4.272 0.497
ATF6B 37 4.223 0.503
HOXA1 63 4.072 0.507
JUN::JUNB(var.2) 36 3.931 0.509
Sp7 36 3.931 0.519
NKX6-3 41 3.916 0.509
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (1390 x2 anchors)
CTCF(+) RAD21(-)  41 (2.95%) LA
 43 (3.09%) RA
 7 (0.5%) LA & RA
CTCF(-) RAD21(+)  45 (3.24%) LA
 50 (3.6%) RA
 10 (0.72%) LA & RA
CTCF(+) RAD21(+)  232 (16.69%) LA
 224 (16.12%) RA
 136 (9.78%) LA + RA
CTCF directionality
(1390 cases)		  20 (1.44%)Convergent ≫ ≪
 5 (0.36%)Divergent ≪ ≫
 124 (8.92%)Tandem ≫ ≫
 242 (17.41%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CENPB29675.7630.551
FOXL115014.4360.493
NFATC28712.0440.526
FOXI113611.7560.496
FOXO413611.7560.489
FOXO613611.7560.498
MEIS115711.6930.482
FOXP313511.5040.497
HOXB48010.8620.454
HOXD48110.7370.458
 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