Information
Accession GMS-65-34 (FID: 481)Browse (ALL)
Title Hi-C on H1 cells - protocol variations
HiC file 4DNFIRZA6EV6 (1.94 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-16 21:20:48
Last update date2025-01-16 21:20:48
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
Submit date 2025-01-16 21:20:49
Reference hg38 (Human)  
Result file DomainCall.tar.gz (223.90 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 1368 domains
2649 boundaries
GMS Loop 4168 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (2649)
CTCF(+) RAD21(-)  85 (3.21%)
CTCF(-) RAD21(+)  72 (2.72%)
CTCF(+) RAD21(+)  319 (12.04%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 66 7.657 0.540
ZBTB2 56 4.970 0.541
VAX1 71 3.823 0.524
Arid3a 65 3.740 0.527
HOXB5 75 3.616 0.517
VAX2 55 3.430 0.522
GSX2 52 3.184 0.516
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (4168 x2 anchors)
CTCF(+) RAD21(-)  145 (3.48%) LA
 140 (3.36%) RA
 2 (0.05%) LA & RA
CTCF(-) RAD21(+)  130 (3.12%) LA
 152 (3.65%) RA
 3 (0.07%) LA & RA
CTCF(+) RAD21(+)  660 (15.83%) LA
 709 (17.01%) RA
 145 (3.48%) LA + RA
CTCF directionality
(4168 cases)		  128 (3.07%)Convergent ≫ ≪
 11 (0.26%)Divergent ≪ ≫
 69 (1.66%)Tandem ≫ ≫
 1238 (29.7%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Arid3a35528.5450.520
CTCF25523.5500.552
FOXL142521.9840.534
NFATC228421.6850.561
Foxj231820.3380.512
ZBTB223820.1450.552
Nr2e339220.0090.515
FOXI139619.5290.525
FOXO439619.5290.525
FOXO639619.5290.525
 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