Information
Accession GMS-65-41 (FID: 488)Browse (ALL)
Title Hi-C on H1 cells - protocol variations
HiC file 4DNFIIMZB6Y9 (15.49 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-17 05:48:13
Last update date2025-01-17 05:48:13
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 2025-01-17 05:48:14
Reference hg38 (Human)  
Result file DomainCall.tar.gz (442.23 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 14317 domains
23162 boundaries
GMS Loop 22749 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (23162)
CTCF(+) RAD21(-)  831 (3.59%)
CTCF(-) RAD21(+)  727 (3.14%)
CTCF(+) RAD21(+)  3432 (14.82%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 718 33.928 0.549
ZBTB2 710 33.111 0.545
Arid3a 700 21.399 0.539
MEIS1 1099 20.929 0.503
RHOXF1 725 19.347 0.516
Dlx2 565 15.879 0.512
FOXL1 925 13.512 0.522
FOXP3 891 12.899 0.519
Nr2e3 870 12.878 0.506
FOXI1 886 12.779 0.525
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (22749 x2 anchors)
CTCF(+) RAD21(-)  991 (4.36%) LA
 1046 (4.6%) RA
 54 (0.24%) LA & RA
CTCF(-) RAD21(+)  750 (3.3%) LA
 844 (3.71%) RA
 36 (0.16%) LA & RA
CTCF(+) RAD21(+)  5937 (26.1%) LA
 5994 (26.35%) RA
 2087 (9.17%) LA + RA
CTCF directionality
(22781 cases)		  1915 (8.41%)Convergent ≫ ≪
 90 (0.4%)Divergent ≪ ≫
 821 (3.6%)Tandem ≫ ≫
 8380 (36.79%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF3343175.2610.630
ZBTB22712126.7600.610
Sox5372366.3190.559
Arid3a198747.1600.556
Nr2e3232544.0410.508
FOXL1240043.4330.527
NFATC2160241.1170.571
FOXP3227139.3760.527
FOXO4226138.8910.532
FOXI1226238.6210.535
 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