Information
Accession GMS-64-80 (FID: 670)Browse (ALL)
Title Hi-C on WTC-11 differentiated to cardiac muscle cell
HiC file 4DNFIH1NZ1M8 (5.44 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-18 15:37:09
Last update date2025-02-18 15:37:09
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 15:37:09
Reference hg38 (Human)  
Result file DomainCall.tar.gz (362.29 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 8051 domains
14032 boundaries
GMS Loop 18498 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (14032)
CTCF(+) RAD21(-)  477 (3.4%)
CTCF(-) RAD21(+)  376 (2.68%)
CTCF(+) RAD21(+)  1862 (13.27%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 472 35.172 0.547
ZBTB2 430 28.819 0.545
Sox5 757 13.667 0.544
MEIS1 566 10.653 0.503
FOXP3 463 10.408 0.515
FOXI1 462 10.322 0.520
FOXO4 462 10.322 0.519
FOXO6 462 10.167 0.518
FOXL1 474 9.965 0.514
Arid3a 351 8.100 0.540
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (18498 x2 anchors)
CTCF(+) RAD21(-)  722 (3.9%) LA
 704 (3.81%) RA
 30 (0.16%) LA & RA
CTCF(-) RAD21(+)  685 (3.7%) LA
 622 (3.36%) RA
 34 (0.18%) LA & RA
CTCF(+) RAD21(+)  4879 (26.38%) LA
 4990 (26.98%) RA
 1726 (9.33%) LA + RA
CTCF directionality
(18526 cases)		  1550 (8.37%)Convergent ≫ ≪
 53 (0.29%)Divergent ≪ ≫
 626 (3.38%)Tandem ≫ ≫
 6893 (37.21%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF2378138.9200.631
ZBTB22259128.1190.612
FOXL1174727.0530.530
FOXI1166925.6680.534
FOXO4166925.6680.532
FOXO6166925.6680.531
FOXP3166925.6680.528
HOXB6156921.2790.515
Foxj2119619.9980.516
PRRX1140418.8530.505
 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