Information
Accession GMS-65-28 (FID: 475)Browse (ALL)
Title Hi-C on H1 cells - protocol variations
HiC file 4DNFIE8T8JZ8 (1.41 GB)
 hic mCool Cooler-Tree
Submit date2025-01-16 18:22:22
Last update date2025-01-16 18:22:22
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 18:22:23
Reference hg38 (Human)  
Result file DomainCall.tar.gz (206.89 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 2656 domains
5020 boundaries
GMS Loop 5033 loops
 Hi-C map is too sparse
Motifs in 5Kb Boundaries (5020)
CTCF(+) RAD21(-)  179 (3.57%)
CTCF(-) RAD21(+)  152 (3.03%)
CTCF(+) RAD21(+)  591 (11.77%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue
ROC
AUC
Sox5 304 14.685 0.553
CTCF 125 11.254 0.536
ZNF354C 177 10.520 0.474
ZBTB2 115 9.054 0.539
NFATC2 120 8.116 0.544
VSX2 134 7.305 0.514
VSX1 109 7.106 0.515
HOXB1 177 6.907 0.516
HOXC4 176 6.856 0.510
HOXB5 156 6.503 0.519
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (5033 x2 anchors)
CTCF(+) RAD21(-)  206 (4.09%) LA
 215 (4.27%) RA
 16 (0.32%) LA & RA
CTCF(-) RAD21(+)  165 (3.28%) LA
 167 (3.32%) RA
 3 (0.06%) LA & RA
CTCF(+) RAD21(+)  869 (17.27%) LA
 838 (16.65%) RA
 190 (3.78%) LA + RA
CTCF directionality
(5033 cases)
 169 (3.36%)Convergent ≫ ≪
 17 (0.34%)Divergent ≪ ≫
 102 (2.03%)Tandem ≫ ≫
 1552 (30.84%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue
ROC
AUC
CTCF35233.8610.555
Sox572332.8570.560
ZBTB231827.3350.547
FOXL152425.6330.523
NFATC234623.4680.564
FOXI149823.3740.527
FOXO449823.3740.526
FOXO649823.3740.525
FOXP349823.3740.523
NKX6-146922.5490.509
 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