Information
Accession GMS-65-37 (FID: 484)Browse (ALL)
Title Hi-C on H1 cells
HiC file 4DNFIGY85S4W (3.50 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-17 11:17:58
Last update date2025-01-17 11:17:58
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 00:43:29
Reference hg38 (Human)  
Result file DomainCall.tar.gz (336.08 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 8696 domains
15357 boundaries
GMS Loop 11618 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (15357)
CTCF(+) RAD21(-)  428 (2.79%)
CTCF(-) RAD21(+)  533 (3.47%)
CTCF(+) RAD21(+)  2031 (13.23%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 450 26.839 0.542
ZBTB2 432 24.447 0.542
Sox5 846 17.290 0.542
NFATC2 354 11.800 0.537
MEIS1 1159 10.801 0.518
FOXL1 548 9.824 0.518
FOXI1 521 8.826 0.524
FOXO4 521 8.826 0.523
FOXO6 521 8.826 0.522
FOXP3 521 8.826 0.521
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (11618 x2 anchors)
CTCF(+) RAD21(-)  418 (3.6%) LA
 417 (3.59%) RA
 20 (0.17%) LA & RA
CTCF(-) RAD21(+)  420 (3.62%) LA
 435 (3.74%) RA
 17 (0.15%) LA & RA
CTCF(+) RAD21(+)  2491 (21.44%) LA
 2487 (21.41%) RA
 679 (5.84%) LA + RA
CTCF directionality
(11624 cases)		  620 (5.33%)Convergent ≫ ≪
 35 (0.3%)Divergent ≪ ≫
 264 (2.27%)Tandem ≫ ≫
 3987 (34.3%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF1312103.9700.596
ZBTB2108375.0470.582
Sox5174744.0030.564
FOXL1121037.1690.526
FOXI1115033.5400.530
FOXO6115033.5400.528
FOXO4114933.4560.528
FOXP3114933.4560.524
MEIS1123831.2910.511
NFATC271930.3860.559
 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