Information
Accession GMS-64-65 (FID: 649)Browse (ALL)
Title Hi-C on HUVEC cell
HiC file 4DNFI9VXTBE2 (3.52 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-11 12:03:11
Last update date2025-02-11 12:03:11
Contact Sung-Joon PARK
park 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 2025-02-11 12:03:11
Reference hg38 (Human)  
Result file DomainCall.tar.gz (248.27 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3629 domains
6767 boundaries
GMS Loop 5118 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (6767)
CTCF(+) RAD21(-)  237 (3.5%)
CTCF(-) RAD21(+)  181 (2.67%)
CTCF(+) RAD21(+)  906 (13.39%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5 472 19.534 0.528
ZNF354C 295 17.445 0.491
Arid3a 220 13.785 0.558
VSX1 293 12.804 0.508
FOXL1 306 12.307 0.522
FOXP3 293 12.262 0.525
HOXB6 294 12.143 0.522
FOXI1 292 12.116 0.530
FOXO6 292 12.116 0.528
FOXO4 291 11.971 0.529
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (5118 x2 anchors)
CTCF(+) RAD21(-)  187 (3.65%) LA
 176 (3.44%) RA
 5 (0.1%) LA & RA
CTCF(-) RAD21(+)  136 (2.66%) LA
 159 (3.11%) RA
 7 (0.14%) LA & RA
CTCF(+) RAD21(+)  791 (15.46%) LA
 787 (15.38%) RA
 171 (3.34%) LA + RA
CTCF directionality
(5118 cases)		  139 (2.72%)Convergent ≫ ≪
 19 (0.37%)Divergent ≪ ≫
 90 (1.76%)Tandem ≫ ≫
 1445 (28.23%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C111256.8400.553
MEIS163237.0970.522
Nr2e355433.1330.514
CTCF35032.5420.546
RHOXF148232.0210.515
FOXL155831.1000.528
FOXI152428.0290.524
FOXO452428.0290.522
FOXO652428.0290.522
FOXP352428.0290.519
 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