Information
Accession GMS-65-21 (FID: 467)Browse (ALL)
Title Liquified Chromatin Hi-C on K562 cells
HiC file 4DNFIZBXXJAF (6.09 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-16 11:39:31
Last update date2025-01-16 11:39:31
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 11:39:32
Reference hg38 (Human)  
Result file DomainCall.tar.gz (184.96 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 514 domains
984 boundaries
GMS Loop 528 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (984)
CTCF(+) RAD21(-)  22 (2.24%)
CTCF(-) RAD21(+)  36 (3.66%)
CTCF(+) RAD21(+)  100 (10.16%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ISX 30 4.508 0.497
Shox2 27 3.776 0.498
SHOX 26 3.589 0.495
RAX2 26 3.439 0.495
Sox5 58 3.342 0.544
ZNF354C 77 3.323 0.469
CTCF 23 3.287 0.513
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (528 x2 anchors)
CTCF(+) RAD21(-)  24 (4.55%) LA
 22 (4.17%) RA
 2 (0.38%) LA & RA
CTCF(-) RAD21(+)  11 (2.08%) LA
 24 (4.55%) RA
 0 (0%) LA & RA
CTCF(+) RAD21(+)  61 (11.55%) LA
 74 (14.02%) RA
 16 (3.03%) LA + RA
CTCF directionality
(528 cases)		  11 (2.08%)Convergent ≫ ≪
 5 (0.95%)Divergent ≪ ≫
 11 (2.08%)Tandem ≫ ≫
 127 (24.05%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C13651.7200.515
Arid3a9032.9690.523
NFATC27728.2910.544
MEIS110325.9610.523
Sox511621.6140.534
FOXL15920.0640.486
Nr2e38319.8330.492
RHOXF18119.2500.503
Dlx25615.3630.488
FOXI16110.9640.493
 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