Information
Accession GMS-64-66 (FID: 650)Browse (ALL)
Title Hi-C on WTC-11 differentiated to cardiac muscle cell
HiC file 4DNFI7ST3KR1 (4.22 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-18 15:15:05
Last update date2025-02-18 15:15:05
Contact Sung-Joon PARK
park AT hgc.jp
The University of Tokyo
Sharingopen access
Keywords Hi-C  4DN  contact matrix 
 Domain/Loop Calling Information

URL copied to the clipboard
Submit date 2025-02-18 15:15:06
Reference hg38 (Human)  
Result file DomainCall.tar.gz (379.48 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 7867 domains
13784 boundaries
GMS Loop 21637 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (13784)
CTCF(+) RAD21(-)  521 (3.78%)
CTCF(-) RAD21(+)  323 (2.34%)
CTCF(+) RAD21(+)  1905 (13.82%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 446 32.226 0.547
ZBTB2 397 24.934 0.545
RHOXF1 459 9.208 0.515
Nobox 388 8.561 0.517
HOXB6 478 8.256 0.514
HOXB1 439 7.893 0.513
GATA3 516 7.812 0.515
ZNF518A 713 7.672 0.521
FOXN3 457 7.450 0.520
PRRX2 460 7.422 0.511
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (21637 x2 anchors)
CTCF(+) RAD21(-)  896 (4.14%) LA
 881 (4.07%) RA
 50 (0.23%) LA & RA
CTCF(-) RAD21(+)  745 (3.44%) LA
 704 (3.25%) RA
 33 (0.15%) LA & RA
CTCF(+) RAD21(+)  5901 (27.27%) LA
 5952 (27.51%) RA
 2150 (9.94%) LA + RA
CTCF directionality
(21666 cases)		  1970 (9.09%)Convergent ≫ ≪
 67 (0.31%)Divergent ≪ ≫
 738 (3.41%)Tandem ≫ ≫
 8138 (37.56%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF3201175.9530.633
ZBTB22674133.3850.616
Sox5309035.6630.533
MEIS1387930.4620.514
FOXL1201826.8920.529
FOXI1193524.8160.533
FOXO4193524.8160.530
FOXO6193524.8160.530
FOXP3193924.4870.528
NKX6-1194123.3480.513
 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