Information
Accession GMS-64-78 (FID: 668)Browse (ALL)
Title Hi-C on WTC-11 cardiac differention timecourse
HiC file 4DNFIH6ANSX9 (4.84 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-18 15:30:04
Last update date2025-02-18 15:30:04
Contact Sung-Joon PARK
park 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 2025-02-18 15:30:04
Reference hg38 (Human)  
Result file DomainCall.tar.gz (373.46 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 7971 domains
13948 boundaries
GMS Loop 21398 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (13948)
CTCF(+) RAD21(-)  420 (3.01%)
CTCF(-) RAD21(+)  427 (3.06%)
CTCF(+) RAD21(+)  1925 (13.8%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB2 428 28.848 0.542
CTCF 415 26.941 0.545
Sox5 759 11.521 0.540
MEIS1 581 10.839 0.511
FOXL1 500 9.838 0.517
Nr2e3 446 9.630 0.518
FOXI1 483 9.604 0.520
FOXO4 483 9.604 0.519
FOXO6 483 9.604 0.519
RHOXF1 404 9.580 0.515
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (21398 x2 anchors)
CTCF(+) RAD21(-)  926 (4.33%) LA
 916 (4.28%) RA
 53 (0.25%) LA & RA
CTCF(-) RAD21(+)  723 (3.38%) LA
 704 (3.29%) RA
 31 (0.14%) LA & RA
CTCF(+) RAD21(+)  5945 (27.78%) LA
 5891 (27.53%) RA
 2066 (9.66%) LA + RA
CTCF directionality
(21426 cases)		  1946 (9.08%)Convergent ≫ ≪
 77 (0.36%)Divergent ≪ ≫
 700 (3.27%)Tandem ≫ ≫
 8288 (38.68%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF3536206.9980.639
ZBTB22785144.4640.617
MEIS1383132.1350.509
FOXL1196126.3400.522
FOXI1186624.9720.528
FOXO4186624.9720.525
FOXO6186624.9720.518
FOXP3186524.9280.522
Nr2e3176722.1850.515
ZNF354C171621.4820.492
 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