Information
Accession GMS-65-39 (FID: 486)Browse (ALL)
Title Hi-C on H1 cells
HiC file 4DNFI2LTNXME (3.84 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-17 12:55:57
Last update date2025-01-17 12:55:57
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 02:26:07
Reference hg38 (Human)  
Result file DomainCall.tar.gz (312.00 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 7615 domains
13526 boundaries
GMS Loop 8722 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (13526)
CTCF(+) RAD21(-)  436 (3.22%)
CTCF(-) RAD21(+)  467 (3.45%)
CTCF(+) RAD21(+)  1836 (13.57%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 363 21.002 0.546
MEIS1 615 17.822 0.505
ZBTB2 338 17.622 0.542
RHOXF1 493 15.658 0.505
NFATC2 328 15.541 0.540
HOXB6 524 13.847 0.511
Nr2e3 505 12.728 0.510
HOXB1 471 10.307 0.512
FOXL1 505 10.267 0.514
FOXP3 485 9.744 0.515
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (8722 x2 anchors)
CTCF(+) RAD21(-)  387 (4.44%) LA
 353 (4.05%) RA
 26 (0.3%) LA & RA
CTCF(-) RAD21(+)  280 (3.21%) LA
 291 (3.34%) RA
 14 (0.16%) LA & RA
CTCF(+) RAD21(+)  1705 (19.55%) LA
 1708 (19.58%) RA
 430 (4.93%) LA + RA
CTCF directionality
(8725 cases)		  380 (4.36%)Convergent ≫ ≪
 39 (0.45%)Divergent ≪ ≫
 207 (2.37%)Tandem ≫ ≫
 2907 (33.32%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF82371.5430.571
ZBTB268751.3710.560
Sox5145948.9980.566
Nr2e391043.1420.512
FOXL197341.1320.527
FOXP392238.1060.525
FOXI192137.9960.531
FOXO492137.9960.528
FOXO692137.7080.529
NFATC260631.4280.567
 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