Information
Accession GMS-65-20 (FID: 499)Browse (ALL)
Title HiC on K562 cells +/- Heat Shock
HiC file 4DNFI8Y9SRP2 (1.58 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 2025-01-17 11:06:51
Reference hg38 (Human)  
Result file DomainCall.tar.gz (241.69 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 2235 domains
4304 boundaries
GMS Loop 4894 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (4304)
CTCF(+) RAD21(-)  134 (3.11%)
CTCF(-) RAD21(+)  141 (3.28%)
CTCF(+) RAD21(+)  538 (12.5%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 126 15.225 0.541
Sox5 280 13.263 0.566
Nr2e3 179 8.677 0.504
FOXO3 158 7.934 0.521
ZBTB2 96 7.729 0.538
FOXN3 152 7.593 0.555
Shox2 96 6.423 0.511
ISX 89 6.124 0.509
FOXO4 159 6.086 0.528
FOXP3 159 6.086 0.523
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (4894 x2 anchors)
CTCF(+) RAD21(-)  176 (3.6%) LA
 177 (3.62%) RA
 11 (0.22%) LA & RA
CTCF(-) RAD21(+)  175 (3.58%) LA
 187 (3.82%) RA
 8 (0.16%) LA & RA
CTCF(+) RAD21(+)  769 (15.71%) LA
 871 (17.8%) RA
 174 (3.56%) LA + RA
CTCF directionality
(4894 cases)		  141 (2.88%)Convergent ≫ ≪
 19 (0.39%)Divergent ≪ ≫
 96 (1.96%)Tandem ≫ ≫
 1481 (30.26%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
MEIS160337.1630.509
FOXL156034.0410.533
Nr2e351832.0720.515
FOXI153431.0560.533
FOXO453431.0560.531
FOXO653431.0560.530
FOXP353431.0560.527
Foxj241230.0120.512
CTCF32429.8750.542
NFATC234826.3050.576
 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