Information
Accession GMS-65-96 (FID: 548)Browse (ALL)
Title Hi-C on sync. HeLa cells - Rep2
HiC file 4DNFIJ3DZPGM (1.17 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-18 09:12:41
Last update date2025-01-18 09:12:41
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 2025-01-18 09:12:41
Reference hg38 (Human)  
Result file DomainCall.tar.gz (205.28 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 716 domains
1413 boundaries
GMS Loop 2478 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (1413)
CTCF(+) RAD21(-)  46 (3.26%)
CTCF(-) RAD21(+)  41 (2.9%)
CTCF(+) RAD21(+)  155 (10.97%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
HOXB1 50 4.230 0.521
RHOXF1 53 4.012 0.521
HOXB6 52 3.642 0.526
Foxj2 41 3.242 0.514
NR2C1 30 3.089 0.533
FOXK1 29 3.036 0.498
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (2478 x2 anchors)
CTCF(+) RAD21(-)  106 (4.28%) LA
 98 (3.95%) RA
 4 (0.16%) LA & RA
CTCF(-) RAD21(+)  77 (3.11%) LA
 79 (3.19%) RA
 3 (0.12%) LA & RA
CTCF(+) RAD21(+)  371 (14.97%) LA
 363 (14.65%) RA
 55 (2.22%) LA + RA
CTCF directionality
(2478 cases)		  40 (1.61%)Convergent ≫ ≪
 6 (0.24%)Divergent ≪ ≫
 40 (1.61%)Tandem ≫ ≫
 766 (30.91%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox543937.0610.578
ZNF354C31033.0240.541
Nr2e327728.1300.521
RHOXF127426.0130.523
FOXI125524.2790.538
FOXO425524.2790.537
FOXP325524.2790.533
FOXO625524.0880.536
FOXL117624.0040.534
MEIS127919.5070.511
 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