Information
Accession GMS-65-19 (FID: 465)Browse (ALL)
Title Liquified Chromatin Hi-C on K562 cells
HiC file 4DNFIH2A7IKF (4.24 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-16 11:34:58
Last update date2025-01-16 11:34:58
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 11:34:59
Reference hg38 (Human)  
Result file DomainCall.tar.gz (228.36 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 2622 domains
4803 boundaries
GMS Loop 2977 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (4803)
CTCF(+) RAD21(-)  160 (3.33%)
CTCF(-) RAD21(+)  177 (3.69%)
CTCF(+) RAD21(+)  642 (13.37%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5 370 29.746 0.571
RHOXF1 203 17.141 0.518
Nr2e3 234 16.833 0.523
ZNF354C 254 16.509 0.500
FOXI1 210 15.353 0.535
FOXO4 210 15.353 0.533
FOXO6 210 15.353 0.532
FOXP3 210 15.353 0.529
ZNF518A 315 14.589 0.530
NFATC2 149 13.624 0.565
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (2977 x2 anchors)
CTCF(+) RAD21(-)  112 (3.76%) LA
 107 (3.59%) RA
 6 (0.2%) LA & RA
CTCF(-) RAD21(+)  80 (2.69%) LA
 86 (2.89%) RA
 5 (0.17%) LA & RA
CTCF(+) RAD21(+)  419 (14.07%) LA
 459 (15.42%) RA
 98 (3.29%) LA + RA
CTCF directionality
(2977 cases)		  84 (2.82%)Convergent ≫ ≪
 8 (0.27%)Divergent ≪ ≫
 65 (2.18%)Tandem ≫ ≫
 783 (26.3%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox549938.3030.541
RHOXF129829.5910.520
MEIS136427.9170.506
NFATC223627.3100.551
FOXL132724.9270.524
FOXP331123.4890.516
FOXI131023.4690.522
FOXO431023.4690.519
FOXO631023.4690.519
Nr2e329919.8490.506
 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