Information
Accession GMS-65-38 (FID: 485)Browse (ALL)
Title Hi-C on H1 cells
HiC file 4DNFI6Z3L9J7 (3.63 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-17 11:44:32
Last update date2025-01-17 11:44:32
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 01:16:39
Reference hg38 (Human)  
Result file DomainCall.tar.gz (307.86 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 7772 domains
13674 boundaries
GMS Loop 8577 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (13674)
CTCF(+) RAD21(-)  567 (4.15%)
CTCF(-) RAD21(+)  350 (2.56%)
CTCF(+) RAD21(+)  1829 (13.38%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 378 22.613 0.548
ZBTB2 357 19.719 0.543
Sox5 837 13.757 0.547
ZNF354C 498 13.467 0.500
HOXB1 471 13.149 0.516
VAX1 414 12.058 0.517
MEIS1 607 11.848 0.507
PRRX1 498 11.172 0.508
NFATC2 313 10.916 0.545
Arid3a 386 10.408 0.540
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (8577 x2 anchors)
CTCF(+) RAD21(-)  358 (4.17%) LA
 338 (3.94%) RA
 23 (0.27%) LA & RA
CTCF(-) RAD21(+)  234 (2.73%) LA
 252 (2.94%) RA
 4 (0.05%) LA & RA
CTCF(+) RAD21(+)  1654 (19.28%) LA
 1662 (19.38%) RA
 417 (4.86%) LA + RA
CTCF directionality
(8577 cases)		  380 (4.43%)Convergent ≫ ≪
 32 (0.37%)Divergent ≪ ≫
 179 (2.09%)Tandem ≫ ≫
 2830 (33%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF92289.1200.577
ZBTB271556.9060.566
Sox5135047.2830.567
NKX6-183730.9290.508
FOXL187628.6160.528
FOXI183927.1250.532
FOXO483927.1250.532
FOXO683927.1250.531
FOXP383927.1250.526
NFATC257626.9590.567
 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