Information
Accession GMS-65-33 (FID: 480)Browse (ALL)
Title Hi-C on H1 cells - protocol variations
HiC file 4DNFIOX3BGNE (5.62 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-16 21:05:04
Last update date2025-01-16 21:05:04
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 2025-01-16 21:05:05
Reference hg38 (Human)  
Result file DomainCall.tar.gz (265.70 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 4582 domains
8438 boundaries
GMS Loop 6136 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (8438)
CTCF(+) RAD21(-)  242 (2.87%)
CTCF(-) RAD21(+)  278 (3.29%)
CTCF(+) RAD21(+)  1171 (13.88%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB2 257 23.448 0.540
CTCF 242 20.465 0.543
Nr2e3 306 11.660 0.514
Sox5 463 10.932 0.540
NFATC2 200 10.412 0.546
MEIS1 335 8.808 0.515
RHOXF1 268 7.942 0.514
VSX1 313 7.491 0.506
Arid3a 218 7.218 0.561
FOXL1 311 6.566 0.514
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (6136 x2 anchors)
CTCF(+) RAD21(-)  221 (3.6%) LA
 219 (3.57%) RA
 13 (0.21%) LA & RA
CTCF(-) RAD21(+)  181 (2.95%) LA
 208 (3.39%) RA
 8 (0.13%) LA & RA
CTCF(+) RAD21(+)  923 (15.04%) LA
 935 (15.24%) RA
 204 (3.32%) LA + RA
CTCF directionality
(6136 cases)		  178 (2.9%)Convergent ≫ ≪
 20 (0.33%)Divergent ≪ ≫
 96 (1.56%)Tandem ≫ ≫
 1710 (27.87%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox591633.5310.554
CTCF39630.8040.549
ZBTB235724.5140.543
Nr2e358822.1090.524
MEIS165420.2490.514
FOXL160619.3490.519
ZNF354C46019.2390.502
RHOXF148719.1200.511
NFATC238718.3700.558
FOXP358018.1440.517
 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