Information
Accession GMS-65-16 (FID: 462)Browse (ALL)
Title Liquified Chromatin Hi-C on K562 cells
HiC file 4DNFIPAF4PYT (3.18 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-16 11:30:55
Last update date2025-01-16 11:30:55
Contact GMSuite GENOMEMODALITY
gmsuite 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 2025-01-16 11:30:56
Reference hg38 (Human)  
Result file DomainCall.tar.gz (232.89 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 2465 domains
4560 boundaries
GMS Loop 5951 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (4560)
CTCF(+) RAD21(-)  140 (3.07%)
CTCF(-) RAD21(+)  131 (2.87%)
CTCF(+) RAD21(+)  526 (11.54%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 96 6.795 0.534
ZBTB2 87 5.068 0.532
MEIS1 158 3.690 0.496
EMX1 123 3.661 0.505
NR2F6(var.3) 78 3.550 0.510
HOXB2 93 3.359 0.509
HOXD3 93 3.359 0.511
GSX2 94 3.185 0.508
PDX1 87 3.162 0.505
HOXB5 120 3.031 0.518
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (5951 x2 anchors)
CTCF(+) RAD21(-)  192 (3.23%) LA
 168 (2.82%) RA
 7 (0.12%) LA & RA
CTCF(-) RAD21(+)  211 (3.55%) LA
 203 (3.41%) RA
 11 (0.18%) LA & RA
CTCF(+) RAD21(+)  762 (12.8%) LA
 752 (12.64%) RA
 128 (2.15%) LA + RA
CTCF directionality
(5951 cases)		  99 (1.66%)Convergent ≫ ≪
 22 (0.37%)Divergent ≪ ≫
 71 (1.19%)Tandem ≫ ≫
 1490 (25.04%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Nr2e371446.8820.521
Sox592645.6130.559
FOXL159730.5040.531
FOXI157430.2940.531
FOXO457430.2940.527
FOXO657430.2940.527
FOXP357430.2940.522
CTCF33422.3200.536
Foxj239919.9210.511
UNCX32618.5700.520
 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