Information
Accession GMS-65-107 (FID: 559)Browse (ALL)
Title Hi-C on sync. HeLa cells - Rep2
HiC file 4DNFI5ERM9J7 (1.41 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-18 15:28:52
Last update date2025-01-18 15:28:52
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 15:28:52
Reference hg38 (Human)  
Result file DomainCall.tar.gz (210.86 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 1001 domains
1953 boundaries
GMS Loop 2622 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (1953)
CTCF(+) RAD21(-)  66 (3.38%)
CTCF(-) RAD21(+)  65 (3.33%)
CTCF(+) RAD21(+)  234 (11.98%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
VAX1 67 6.242 0.507
VAX2 50 6.174 0.507
GSX2 49 6.149 0.509
CTCF 47 5.721 0.538
Nobox 59 5.624 0.507
Nr2e3 71 5.495 0.511
HOXB2 46 5.418 0.504
HOXD3 46 5.418 0.511
HOXB1 76 5.282 0.518
ZBTB2 45 5.122 0.539
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (2622 x2 anchors)
CTCF(+) RAD21(-)  97 (3.7%) LA
 110 (4.2%) RA
 6 (0.23%) LA & RA
CTCF(-) RAD21(+)  74 (2.82%) LA
 86 (3.28%) RA
 3 (0.11%) LA & RA
CTCF(+) RAD21(+)  393 (14.99%) LA
 419 (15.98%) RA
 65 (2.48%) LA + RA
CTCF directionality
(2622 cases)		  56 (2.14%)Convergent ≫ ≪
 8 (0.31%)Divergent ≪ ≫
 44 (1.68%)Tandem ≫ ≫
 803 (30.63%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox546040.4090.573
FOXL133040.2130.534
FOXI130935.7790.538
FOXO430935.7790.534
FOXO630935.7790.534
FOXP330935.7790.529
Nr2e330532.6620.516
ZNF354C24629.6120.522
RHOXF126428.4640.521
NFATC219527.8010.576
 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