Information
Accession GMS-65-12 (FID: 474)Browse (ALL)
Title HiC on K562 cells +/- Heat Shock
HiC file 4DNFI5XOESBI (1.37 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 17:29:19
Reference hg38 (Human)  
Result file DomainCall.tar.gz (229.05 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 1862 domains
3603 boundaries
GMS Loop 3984 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (3603)
CTCF(+) RAD21(-)  118 (3.28%)
CTCF(-) RAD21(+)  123 (3.41%)
CTCF(+) RAD21(+)  417 (11.57%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB2 89 9.102 0.529
CTCF 85 8.087 0.534
LHX5 86 7.795 0.512
UNCX 152 7.576 0.524
RAX2 89 7.484 0.511
Shox2 82 7.354 0.512
ISX 86 6.799 0.512
PRRX2 119 6.379 0.511
LHX9 119 6.379 0.510
VAX1 107 6.041 0.507
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (3984 x2 anchors)
CTCF(+) RAD21(-)  162 (4.07%) LA
 160 (4.02%) RA
 5 (0.13%) LA & RA
CTCF(-) RAD21(+)  101 (2.54%) LA
 107 (2.69%) RA
 4 (0.1%) LA & RA
CTCF(+) RAD21(+)  585 (14.68%) LA
 604 (15.16%) RA
 106 (2.66%) LA + RA
CTCF directionality
(3984 cases)		  94 (2.36%)Convergent ≫ ≪
 11 (0.28%)Divergent ≪ ≫
 61 (1.53%)Tandem ≫ ≫
 1179 (29.59%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C152149.1950.553
Sox566947.3680.575
CTCF29032.9860.543
FOXL144829.8520.529
MEIS145828.6430.505
FOXI142927.9610.529
FOXO442927.9610.528
FOXO642927.9610.527
FOXP342927.9610.524
ZBTB226427.4450.542
 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