Information
Accession GMS-65-12 (FID: 488)Browse (ALL)
4DNFI15FPSQL.hic
Title Hi-C on sync. HeLa cells
Submit date2025-01-11 20:19:57
Last update date2025-01-11 20:19:57
Contact GMSuite GENOMEMODALITY
gmsuite AT hgc.jp
The University of Tokyo
Sharingopen access
Keywords Hi-C  4DN  contact matrix 
 Domain/Loop Calling Information

URL copied to the clipboard
HiC file 4DNFI15FPSQL (1.36 GB)
 hic  mCool   Cooler-Tree
Result file DomainCall.tar.gz (211.51 MB)  
Submit date 2025-01-12 14:20:16
Reference hg38 (Human)  
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(-)  106 (4.1%)
CTCF(-) RAD21(+)  61 (2.36%)
CTCF(+) RAD21(+)  335 (12.95%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox517611.2290.542
ZBTB2719.5310.544
FOXL11179.4540.520
HOXB5969.1280.507
FOXI11108.6570.527
FOXO41108.6570.526
FOXP31108.6570.523
FOXO61108.5680.524
HOXB11108.2220.506
MEIS1957.6310.510
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (2723 x2 anchors)
CTCF(+) RAD21(-)  116 (4.26%) LA
 104 (3.82%) RA
 9 (0.33%) LA&RA
CTCF(-) RAD21(+)  62 (2.28%) LA
 71 (2.61%) RA
 3 (0.11%) LA&RA
CTCF(+) RAD21(+)  356 (13.07%) LA
 378 (13.88%) RA
 59 (2.17%) LA+RA
CTCF directionality
(2723 cases)		  49 (1.8%)Convergent ≫ ≪
 10 (0.37%)Divergent ≪ ≫
 43 (1.58%)Tandem ≫ ≫
 750 (27.54%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C108444.3200.486
Sox549244.2270.574
FOXL132533.8300.522
FOXI131232.8420.528
FOXO431232.8420.522
FOXO631232.8420.521
FOXP331232.8420.518
Arid3a24227.4500.625
Nr2e329427.3930.513
NFATC220624.4690.574
 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