Information
Accession GMS-65-20 (FID: 466)Browse (ALL)
Title HiC on K562 cells +/- Heat Shock
HiC file 4DNFIWDG7ORH (1.38 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-17 11:06:51
Last update date2025-01-17 11:06:51
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 11:35:25
Reference hg38 (Human)  
Result file DomainCall.tar.gz (230.39 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 1898 domains
3669 boundaries
GMS Loop 4360 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (3669)
CTCF(+) RAD21(-)  100 (2.73%)
CTCF(-) RAD21(+)  117 (3.19%)
CTCF(+) RAD21(+)  459 (12.51%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 104 12.852 0.535
ZBTB2 98 11.164 0.526
NR2C1 83 7.186 0.521
ISL2 98 5.541 0.519
Nr2e3 127 5.381 0.503
RHOXF1 98 4.838 0.511
PRRX1 127 4.797 0.498
LHX9 122 4.328 0.500
LBX1 119 4.225 0.502
NKX6-2 120 4.171 0.496
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (4360 x2 anchors)
CTCF(+) RAD21(-)  184 (4.22%) LA
 206 (4.72%) RA
 16 (0.37%) LA & RA
CTCF(-) RAD21(+)  121 (2.78%) LA
 114 (2.61%) RA
 4 (0.09%) LA & RA
CTCF(+) RAD21(+)  688 (15.78%) LA
 727 (16.67%) RA
 146 (3.35%) LA + RA
CTCF directionality
(4360 cases)		  133 (3.05%)Convergent ≫ ≪
 16 (0.37%)Divergent ≪ ≫
 86 (1.97%)Tandem ≫ ≫
 1335 (30.62%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox572342.5490.575
FOXL147431.0560.529
FOXI145430.8460.535
FOXO445430.8460.532
FOXO645430.8460.532
FOXP345430.8460.528
RHOXF138427.0960.524
CTCF27325.2690.543
Foxj234322.5100.505
Nr2e343322.3960.508
 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