Information
Accession GMS-65-38 (FID: 501)Browse (ALL)
Title Hi-C on H1 cells
HiC file 4DNFID162B9J (3.72 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 11:44:33
Reference hg38 (Human)  
Result file DomainCall.tar.gz (310.47 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 7900 domains
13881 boundaries
GMS Loop 8762 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (13881)
CTCF(+) RAD21(-)  460 (3.31%)
CTCF(-) RAD21(+)  411 (2.96%)
CTCF(+) RAD21(+)  1849 (13.32%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5 911 21.968 0.548
ZBTB2 371 20.977 0.542
CTCF 364 20.032 0.547
MEIS1 637 15.729 0.506
Nr2e3 543 15.365 0.512
RHOXF1 527 15.076 0.510
FOXL1 583 14.950 0.527
VAX1 457 13.526 0.513
HOXB1 494 13.495 0.514
FOXI1 555 13.378 0.529
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (8762 x2 anchors)
CTCF(+) RAD21(-)  365 (4.17%) LA
 356 (4.06%) RA
 25 (0.29%) LA & RA
CTCF(-) RAD21(+)  263 (3%) LA
 246 (2.81%) RA
 10 (0.11%) LA & RA
CTCF(+) RAD21(+)  1686 (19.24%) LA
 1630 (18.6%) RA
 407 (4.65%) LA + RA
CTCF directionality
(8764 cases)		  388 (4.43%)Convergent ≫ ≪
 30 (0.34%)Divergent ≪ ≫
 183 (2.09%)Tandem ≫ ≫
 2839 (32.39%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB269151.5560.568
CTCF66648.0240.576
Sox5143347.5080.564
RHOXF184636.9340.519
MEIS199531.7880.526
FOXL194630.6370.524
ZNF354C99229.6120.468
FOXO490528.3400.524
FOXO690528.3400.524
FOXP390428.2440.520
 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