Information
Accession GMS-65-37 (FID: 500)Browse (ALL)
Title Hi-C on H1 cells
HiC file 4DNFIZN7TUZ4 (3.41 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-17 11:17:58
Last update date2025-01-17 11:17:58
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 11:17:58
Reference hg38 (Human)  
Result file DomainCall.tar.gz (327.97 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 8627 domains
15255 boundaries
GMS Loop 11480 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (15255)
CTCF(+) RAD21(-)  480 (3.15%)
CTCF(-) RAD21(+)  471 (3.09%)
CTCF(+) RAD21(+)  2043 (13.39%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 434 25.041 0.546
ZBTB2 424 23.723 0.543
Sox5 874 13.244 0.541
NFATC2 346 10.791 0.537
FOXL1 571 9.515 0.514
FOXI1 547 8.612 0.521
FOXO4 547 8.612 0.514
FOXO6 547 8.612 0.513
FOXP3 547 8.612 0.516
LHX9 517 8.225 0.509
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (11480 x2 anchors)
CTCF(+) RAD21(-)  487 (4.24%) LA
 476 (4.15%) RA
 24 (0.21%) LA & RA
CTCF(-) RAD21(+)  353 (3.07%) LA
 376 (3.28%) RA
 14 (0.12%) LA & RA
CTCF(+) RAD21(+)  2394 (20.85%) LA
 2416 (21.05%) RA
 625 (5.44%) LA + RA
CTCF directionality
(11483 cases)		  604 (5.26%)Convergent ≫ ≪
 40 (0.35%)Divergent ≪ ≫
 260 (2.26%)Tandem ≫ ≫
 3971 (34.58%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF124196.4780.592
ZBTB2115385.2080.584
MEIS1123734.3880.512
FOXI1110126.4400.535
FOXO4110126.4400.533
FOXO6110126.4400.532
FOXP3110126.4400.529
FOXL1114925.7740.532
Nr2e3102022.5230.524
Foxj282521.0110.514
 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