Information
Accession GMS-65-89 (FID: 541)Browse (ALL)
Title Hi-C on sync. HeLa cells - Rep2
HiC file 4DNFI15FPSQL (1.36 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-18 08:19:56
Last update date2025-01-18 08:19:56
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 08:19:57
Reference hg38 (Human)  
Result file DomainCall.tar.gz (214.31 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 1330 domains
2587 boundaries
GMS Loop 2723 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (2587)
CTCF(+) RAD21(-)  99 (3.83%)
CTCF(-) RAD21(+)  77 (2.98%)
CTCF(+) RAD21(+)  339 (13.1%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5 176 9.970 0.545
HOXB5 100 8.774 0.508
FOXL1 117 8.749 0.525
Arid3a 87 8.596 0.532
HOXB1 110 8.481 0.511
FOXI1 110 8.222 0.532
FOXO4 110 8.222 0.525
FOXO6 110 8.222 0.524
FOXP3 110 8.222 0.520
Nr2e3 107 7.698 0.507
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (2723 x2 anchors)
CTCF(+) RAD21(-)  101 (3.71%) LA
 89 (3.27%) RA
 5 (0.18%) LA & RA
CTCF(-) RAD21(+)  93 (3.42%) LA
 98 (3.6%) RA
 6 (0.22%) LA & RA
CTCF(+) RAD21(+)  388 (14.25%) LA
 418 (15.35%) RA
 73 (2.68%) LA + RA
CTCF directionality
(2723 cases)		  54 (1.98%)Convergent ≫ ≪
 11 (0.4%)Divergent ≪ ≫
 45 (1.65%)Tandem ≫ ≫
 776 (28.5%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
MEIS136033.3180.525
ZNF518A45332.7310.532
FOXL132529.9760.525
FOXP331428.8210.520
FOXI131228.5570.527
FOXO431228.5570.525
FOXO631228.5570.525
RHOXF129527.2190.529
Nr2e329425.9900.516
ZNF354C32623.8800.481
 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