Information
Accession GMS-65-105 (FID: 557)Browse (ALL)
Title Hi-C on sync. HeLa cells - Rep2
HiC file 4DNFIZ95S6TR (1.38 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-18 15:25:34
Last update date2025-01-18 15:25:34
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 15:25:34
Reference hg38 (Human)  
Result file DomainCall.tar.gz (207.73 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 1051 domains
2042 boundaries
GMS Loop 2531 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (2042)
CTCF(+) RAD21(-)  63 (3.09%)
CTCF(-) RAD21(+)  64 (3.13%)
CTCF(+) RAD21(+)  230 (11.26%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB2 54 7.431 0.531
Sox5 119 6.678 0.542
VAX1 66 5.693 0.514
RHOXF1 68 5.063 0.525
Foxj2 61 4.483 0.506
CTCF 44 4.424 0.530
HOXC4 56 4.235 0.513
GSX2 46 4.171 0.512
Nr2e3 77 3.930 0.505
NEUROG1 43 3.853 0.491
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (2531 x2 anchors)
CTCF(+) RAD21(-)  86 (3.4%) LA
 103 (4.07%) RA
 3 (0.12%) LA & RA
CTCF(-) RAD21(+)  77 (3.04%) LA
 79 (3.12%) RA
 0 (0%) LA & RA
CTCF(+) RAD21(+)  387 (15.29%) LA
 401 (15.84%) RA
 76 (3%) LA + RA
CTCF directionality
(2531 cases)		  64 (2.53%)Convergent ≫ ≪
 8 (0.32%)Divergent ≪ ≫
 42 (1.66%)Tandem ≫ ≫
 749 (29.59%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
MEIS155130.6870.512
RHOXF128228.8570.521
FOXL129925.0740.519
FOXP328423.4380.524
FOXI128323.2140.531
FOXO428323.0420.528
FOXO628323.0420.529
ZNF518A37321.3300.530
Nr2e327519.8350.517
CTCF15217.6710.544
 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