Information
Accession GMS-65-32 (FID: 479)Browse (ALL)
Title Hi-C on H1 cells - protocol variations
HiC file 4DNFIALNLR78 (2.05 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-16 21:04:54
Last update date2025-01-16 21:04:54
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 2025-01-16 21:04:57
Reference hg38 (Human)  
Result file DomainCall.tar.gz (257.98 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3025 domains
5790 boundaries
GMS Loop 6187 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (5790)
CTCF(+) RAD21(-)  186 (3.21%)
CTCF(-) RAD21(+)  170 (2.94%)
CTCF(+) RAD21(+)  754 (13.02%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
NFATC2 155 12.161 0.542
HOXB1 221 11.089 0.511
CTCF 139 11.055 0.536
FOXN3 204 10.385 0.539
MEIS1 472 9.682 0.506
ZBTB2 132 9.640 0.528
ZNF354C 219 9.637 0.463
Sox5 362 9.552 0.543
VAX1 178 8.104 0.505
FOXL1 228 7.663 0.520
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (6187 x2 anchors)
CTCF(+) RAD21(-)  231 (3.73%) LA
 244 (3.94%) RA
 9 (0.15%) LA & RA
CTCF(-) RAD21(+)  212 (3.43%) LA
 200 (3.23%) RA
 6 (0.1%) LA & RA
CTCF(+) RAD21(+)  1178 (19.04%) LA
 1173 (18.96%) RA
 287 (4.64%) LA + RA
CTCF directionality
(6187 cases)		  262 (4.23%)Convergent ≫ ≪
 18 (0.29%)Divergent ≪ ≫
 131 (2.12%)Tandem ≫ ≫
 2004 (32.39%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF48846.3590.565
FOXL172045.3440.525
FOXI168743.9330.535
FOXO468743.9330.534
FOXO668743.9330.532
FOXP368743.9330.528
MEIS175436.5350.511
RHOXF163035.7050.505
ZNF354C73534.4750.438
ZBTB240632.0070.562
 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