Information
Accession GMS-65-42 (FID: 566)Browse (ALL)
Title Hi-C on H1 cells - protocol variations
HiC file 4DNFIQYQWPF5 (22.16 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 2025-01-23 09:47:36
Reference hg38 (Human)  
Result file DomainCall.tar.gz (325.55 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 9184 domains
15535 boundaries
GMS Loop 11168 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (15535)
CTCF(+) RAD21(-)  519 (3.34%)
CTCF(-) RAD21(+)  442 (2.85%)
CTCF(+) RAD21(+)  2133 (13.73%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5 1012 23.595 0.547
CTCF 425 22.985 0.551
MEIS1 760 19.598 0.512
NFATC2 404 18.053 0.540
RHOXF1 620 15.570 0.512
ZBTB2 344 13.382 0.544
UNCX 358 13.194 0.502
ZNF354C 1165 12.621 0.478
GATA3 664 12.367 0.500
FOXL1 601 11.771 0.508
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (11168 x2 anchors)
CTCF(+) RAD21(-)  432 (3.87%) LA
 484 (4.33%) RA
 28 (0.25%) LA & RA
CTCF(-) RAD21(+)  291 (2.61%) LA
 364 (3.26%) RA
 12 (0.11%) LA & RA
CTCF(+) RAD21(+)  2181 (19.53%) LA
 2199 (19.69%) RA
 606 (5.43%) LA + RA
CTCF directionality
(11174 cases)		  527 (4.72%)Convergent ≫ ≪
 44 (0.39%)Divergent ≪ ≫
 295 (2.64%)Tandem ≫ ≫
 3576 (32%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB299268.2630.566
CTCF89756.7100.575
Nr2e3119547.9980.507
MEIS1133840.9840.527
FOXL1119936.5200.523
FOXO4114435.1360.527
FOXP3114435.1360.522
FOXI1114534.9400.529
FOXO6114534.6600.526
RHOXF1107534.5440.515
 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