Information
Accession GMS-65-40 (FID: 503)Browse (ALL)
Title Hi-C on H1 cells
HiC file 4DNFIC3JD6O2 (5.04 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-17 13:00:51
Last update date2025-01-17 13:00:51
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 13:00:51
Reference hg38 (Human)  
Result file DomainCall.tar.gz (316.45 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 6697 domains
11979 boundaries
GMS Loop 10190 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (11979)
CTCF(+) RAD21(-)  467 (3.9%)
CTCF(-) RAD21(+)  351 (2.93%)
CTCF(+) RAD21(+)  1725 (14.4%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 362 26.475 0.541
ZBTB2 340 22.969 0.538
Nr2e3 428 8.922 0.512
ZNF354C 436 8.578 0.467
LHX9 413 7.653 0.510
MEIS1 518 7.644 0.506
PRRX2 416 7.536 0.512
Dlx2 247 7.428 0.515
TLX2 252 6.976 0.510
LBX1 363 6.595 0.511
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (10190 x2 anchors)
CTCF(+) RAD21(-)  449 (4.41%) LA
 435 (4.27%) RA
 29 (0.28%) LA & RA
CTCF(-) RAD21(+)  348 (3.42%) LA
 334 (3.28%) RA
 15 (0.15%) LA & RA
CTCF(+) RAD21(+)  2369 (23.25%) LA
 2376 (23.32%) RA
 728 (7.14%) LA + RA
CTCF directionality
(10196 cases)		  688 (6.75%)Convergent ≫ ≪
 38 (0.37%)Divergent ≪ ≫
 273 (2.68%)Tandem ≫ ≫
 3643 (35.73%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF100880.7910.599
ZBTB297976.8000.586
Sox5185270.1240.567
ZNF354C129269.0470.458
FOXL1123958.0550.535
FOXI1119156.0140.537
FOXO6119156.0140.532
FOXO4119055.9040.534
FOXP3119055.9040.529
MEIS1129254.4030.514
 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