Information
Accession GMS-64-31 (FID: 598)Browse (ALL)
Title Hi-C on RAD21-AID tagged HCT-116
HiC file 4DNFISNGDB53 (2.15 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-04 14:14:31
Last update date2025-02-04 14:14:31
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 14:14:31
Reference hg38 (Human)  
Result file DomainCall.tar.gz (205.98 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 1947 domains
3699 boundaries
GMS Loop 2658 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (3699)
CTCF(+) RAD21(-)  98 (2.65%)
CTCF(-) RAD21(+)  127 (3.43%)
CTCF(+) RAD21(+)  414 (11.19%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 102 12.107 0.539
ZBTB2 91 9.153 0.537
Nobox 94 5.233 0.524
Nr2e3 115 4.059 0.521
GATA3 145 3.783 0.513
HOXB6 119 3.663 0.524
ZSCAN31 66 3.650 0.498
VSX1 66 3.477 0.513
NKX6-2 114 3.419 0.512
LHX5 71 3.344 0.519
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (2658 x2 anchors)
CTCF(+) RAD21(-)  90 (3.39%) LA
 87 (3.27%) RA
 6 (0.23%) LA & RA
CTCF(-) RAD21(+)  70 (2.63%) LA
 69 (2.6%) RA
 3 (0.11%) LA & RA
CTCF(+) RAD21(+)  295 (11.1%) LA
 335 (12.6%) RA
 69 (2.6%) LA + RA
CTCF directionality
(2658 cases)		  36 (1.35%)Convergent ≫ ≪
 11 (0.41%)Divergent ≪ ≫
 49 (1.84%)Tandem ≫ ≫
 615 (23.14%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C25317.5700.486
FOXL123615.1300.517
FOXI122815.0700.523
FOXO422815.0700.522
FOXO622815.0700.522
FOXP322715.0250.519
Sox535314.8170.548
Arid3a19613.3480.531
Nr2e322112.2060.501
MEIS12489.5200.505
 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