Information
Accession GMS-65-42 (FID: 489)Browse (ALL)
Title Hi-C on H1 cells - protocol variations
HiC file 4DNFI92GEPN1 (6.41 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-21 18:20:08
Last update date2025-01-21 18:20:08
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 2025-01-21 18:20:09
Reference hg38 (Human)  
Result file DomainCall.tar.gz (255.75 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3115 domains
5818 boundaries
GMS Loop 5752 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (5818)
CTCF(+) RAD21(-)  211 (3.63%)
CTCF(-) RAD21(+)  199 (3.42%)
CTCF(+) RAD21(+)  1002 (17.22%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 214 29.309 0.558
Sox5 448 27.217 0.567
ZBTB2 203 26.310 0.550
ZNF354C 310 17.611 0.498
PRRX1 296 16.723 0.510
MEIS1 332 16.378 0.524
NFATC2 180 15.812 0.559
LHX9 267 14.780 0.507
PRRX2 267 14.636 0.508
NKX6-2 248 13.039 0.512
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (5752 x2 anchors)
CTCF(+) RAD21(-)  229 (3.98%) LA
 242 (4.21%) RA
 21 (0.37%) LA & RA
CTCF(-) RAD21(+)  210 (3.65%) LA
 218 (3.79%) RA
 10 (0.17%) LA & RA
CTCF(+) RAD21(+)  1353 (23.52%) LA
 1391 (24.18%) RA
 474 (8.24%) LA + RA
CTCF directionality
(5757 cases)		  409 (7.1%)Convergent ≫ ≪
 29 (0.5%)Divergent ≪ ≫
 183 (3.18%)Tandem ≫ ≫
 1983 (34.45%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5114081.4540.575
CTCF61678.4160.590
ZBTB253260.7390.579
ZNF354C80957.5920.511
Arid3a59957.3270.528
FOXL174555.4190.533
RHOXF167154.3840.519
Nr2e371353.5530.518
FOXG157449.5970.530
FOXI170048.2000.531
 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)
%>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