Information
Accession GMS-65-39 (FID: 502)Browse (ALL)
Title Hi-C on H1 cells
HiC file 4DNFIFWJJC63 (3.76 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 12:55:58
Reference hg38 (Human)  
Result file DomainCall.tar.gz (304.66 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 7471 domains
13310 boundaries
GMS Loop 8506 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (13310)
CTCF(+) RAD21(-)  510 (3.83%)
CTCF(-) RAD21(+)  383 (2.88%)
CTCF(+) RAD21(+)  1796 (13.49%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 443 33.814 0.545
ZBTB2 360 21.282 0.542
ZNF354C 530 17.427 0.472
Sox5 809 14.604 0.547
HOXB6 516 13.135 0.520
NFATC2 337 11.911 0.542
RHOXF1 453 11.320 0.509
Nr2e3 504 10.811 0.507
HOXB1 459 10.155 0.514
FOXL1 512 9.521 0.520
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (8506 x2 anchors)
CTCF(+) RAD21(-)  363 (4.27%) LA
 359 (4.22%) RA
 25 (0.29%) LA & RA
CTCF(-) RAD21(+)  266 (3.13%) LA
 230 (2.7%) RA
 7 (0.08%) LA & RA
CTCF(+) RAD21(+)  1677 (19.72%) LA
 1733 (20.37%) RA
 427 (5.02%) LA + RA
CTCF directionality
(8510 cases)		  361 (4.24%)Convergent ≫ ≪
 42 (0.49%)Divergent ≪ ≫
 215 (2.53%)Tandem ≫ ≫
 2904 (34.12%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF83576.1560.579
Sox5142460.6660.565
ZNF354C179457.9430.515
ZBTB264747.6980.564
FOXL195437.4310.528
MEIS1167535.2580.518
FOXI190635.2230.533
FOXO490635.2230.530
FOXO690635.2230.531
FOXP390834.8980.526
 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