Information
Accession GMS-64-33 (FID: 600)Browse (ALL)
Title Hi-C on RAD21-AID tagged HCT-116
HiC file 4DNFILIM6FDL (19.78 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-04 14:28:42
Last update date2025-02-04 14:28:42
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 14:28:42
Reference hg38 (Human)  
Result file DomainCall.tar.gz (196.15 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 1131 domains
2084 boundaries
GMS Loop 2430 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (2084)
CTCF(+) RAD21(-)  57 (2.74%)
CTCF(-) RAD21(+)  78 (3.74%)
CTCF(+) RAD21(+)  183 (8.78%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
MEIS1 207 11.404 0.490
Arid3a 71 6.559 0.530
HOXA1 79 6.315 0.509
ZNF354C 76 6.302 0.456
HOXB5 67 5.834 0.519
HOXB6 87 5.828 0.499
HOXB1 76 5.733 0.505
NFATC3 53 5.604 0.497
NFATC2 58 5.141 0.549
HOXA5 66 5.013 0.507
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (2430 x2 anchors)
CTCF(+) RAD21(-)  61 (2.51%) LA
 67 (2.76%) RA
 9 (0.37%) LA & RA
CTCF(-) RAD21(+)  41 (1.69%) LA
 34 (1.4%) RA
 6 (0.25%) LA & RA
CTCF(+) RAD21(+)  416 (17.12%) LA
 427 (17.57%) RA
 290 (11.93%) LA + RA
CTCF directionality
(2430 cases)		  18 (0.74%)Convergent ≫ ≪
 20 (0.82%)Divergent ≪ ≫
 276 (11.36%)Tandem ≫ ≫
 343 (14.12%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CENPB959287.9530.590
ZNF39621237.1340.463
Atf120326.6790.490
Arid3a1567.9330.441
ZNF354C3546.2000.517
NFATC21225.4470.466
MYBL2935.2940.523
ZEB1945.1200.436
HOXB4914.5060.412
HOXD41374.4640.415
 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