Information
Accession GMS-65-12 (FID: 458)Browse (ALL)
Title HiC on K562 cells +/- Heat Shock
HiC file 4DNFIP25GZGA (1.56 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-16 11:27:05
Last update date2025-01-16 11:27:05
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 11:27:06
Reference hg38 (Human)  
Result file DomainCall.tar.gz (227.95 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 2009 domains
3879 boundaries
GMS Loop 4180 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (3879)
CTCF(+) RAD21(-)  124 (3.2%)
CTCF(-) RAD21(+)  117 (3.02%)
CTCF(+) RAD21(+)  485 (12.5%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB2 101 10.851 0.532
RAX2 107 9.062 0.504
ISX 93 8.669 0.504
ZNF518A 226 8.513 0.524
Shox2 96 8.399 0.504
PRRX1 142 8.269 0.501
CTCF 90 8.090 0.543
LHX9 145 7.936 0.507
PRRX2 137 7.623 0.509
NKX6-2 129 7.018 0.503
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (4180 x2 anchors)
CTCF(+) RAD21(-)  172 (4.11%) LA
 181 (4.33%) RA
 10 (0.24%) LA & RA
CTCF(-) RAD21(+)  123 (2.94%) LA
 110 (2.63%) RA
 5 (0.12%) LA & RA
CTCF(+) RAD21(+)  650 (15.55%) LA
 694 (16.6%) RA
 127 (3.04%) LA + RA
CTCF directionality
(4180 cases)		  112 (2.68%)Convergent ≫ ≪
 12 (0.29%)Divergent ≪ ≫
 76 (1.82%)Tandem ≫ ≫
 1297 (31.03%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF30834.8750.549
ZBTB230133.2970.542
MEIS148729.9700.511
RHOXF139923.1080.525
FOXL143821.0820.524
Nr2e341620.4380.519
FOXI141720.4100.527
FOXP341920.3540.522
FOXO441720.2300.526
FOXO641720.2300.526
 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