Information
Accession GMS-65-13 (FID: 459)Browse (ALL)
Title Liquified Chromatin Hi-C on K562 cells
HiC file 4DNFIDKJFK2S (2.12 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-16 11:28:20
Last update date2025-01-16 11:28:20
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 11:28:21
Reference hg38 (Human)  
Result file DomainCall.tar.gz (226.57 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 2849 domains
5327 boundaries
GMS Loop 5371 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (5327)
CTCF(+) RAD21(-)  139 (2.61%)
CTCF(-) RAD21(+)  181 (3.4%)
CTCF(+) RAD21(+)  676 (12.69%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 128 10.606 0.533
ZBTB2 122 9.178 0.537
FOXO3 203 5.822 0.517
Nr2e3 159 5.773 0.518
FOXN3 166 4.759 0.524
VAX1 152 4.748 0.507
HOXB1 175 4.581 0.510
HOXB5 144 4.325 0.516
MEIS1 151 3.983 0.505
HOXB2 105 3.961 0.507
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (5371 x2 anchors)
CTCF(+) RAD21(-)  180 (3.35%) LA
 195 (3.63%) RA
 12 (0.22%) LA & RA
CTCF(-) RAD21(+)  148 (2.76%) LA
 156 (2.9%) RA
 7 (0.13%) LA & RA
CTCF(+) RAD21(+)  625 (11.64%) LA
 701 (13.05%) RA
 95 (1.77%) LA + RA
CTCF directionality
(5371 cases)		  75 (1.4%)Convergent ≫ ≪
 13 (0.24%)Divergent ≪ ≫
 77 (1.43%)Tandem ≫ ≫
 1371 (25.53%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox575731.0130.559
Nr2e349623.8270.483
Arid3a36217.4020.551
HOXB538115.8360.515
MEIS148415.8140.517
FOXP347815.2930.520
FOXL149215.2580.522
FOXI147815.1310.526
FOXO447815.1310.525
FOXO647815.1310.524
 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