Information
Accession GMS-65-30 (FID: 477)Browse (ALL)
Title Hi-C on H1 cells - protocol variations
HiC file 4DNFIBT4EAKN (2.44 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-16 18:22:24
Last update date2025-01-16 18:22:24
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 18:22:25
Reference hg38 (Human)  
Result file DomainCall.tar.gz (255.93 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3354 domains
6340 boundaries
GMS Loop 6549 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (6340)
CTCF(+) RAD21(-)  195 (3.08%)
CTCF(-) RAD21(+)  169 (2.67%)
CTCF(+) RAD21(+)  790 (12.46%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB2 218 26.651 0.540
CTCF 203 22.904 0.544
HOXB1 198 4.895 0.521
Nr2e3 195 4.821 0.518
HOXB5 118 4.469 0.518
LHX9 215 4.274 0.510
Sox5 320 4.257 0.536
PRRX2 230 4.196 0.513
ZNF354C 194 4.149 0.472
HOXC9 131 3.966 0.508
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (6549 x2 anchors)
CTCF(+) RAD21(-)  270 (4.12%) LA
 247 (3.77%) RA
 11 (0.17%) LA & RA
CTCF(-) RAD21(+)  207 (3.16%) LA
 194 (2.96%) RA
 5 (0.08%) LA & RA
CTCF(+) RAD21(+)  1252 (19.12%) LA
 1310 (20%) RA
 306 (4.67%) LA + RA
CTCF directionality
(6549 cases)		  284 (4.34%)Convergent ≫ ≪
 28 (0.43%)Divergent ≪ ≫
 145 (2.21%)Tandem ≫ ≫
 2165 (33.06%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF53350.1600.579
Sox5104949.1970.560
FOXL173041.0270.523
FOXP369537.2590.516
FOXI169336.9820.519
FOXO469336.9820.524
FOXO669336.9820.519
ZBTB244835.5960.569
Nr2e365532.6350.516
NFATC246131.2360.564
 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