Information
Accession GMS-64-68 (FID: 652)Browse (ALL)
Title Hi-C on WTC-11 differentiated to cardiac muscle cell
HiC file 4DNFIK9TW97H (4.98 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-18 15:16:12
Last update date2025-02-18 15:16:12
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 15:16:13
Reference hg38 (Human)  
Result file DomainCall.tar.gz (376.39 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 8069 domains
14059 boundaries
GMS Loop 20782 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (14059)
CTCF(+) RAD21(-)  479 (3.41%)
CTCF(-) RAD21(+)  445 (3.17%)
CTCF(+) RAD21(+)  2064 (14.68%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 524 43.317 0.548
ZBTB2 452 31.994 0.546
VSX1 551 13.936 0.513
VSX2 329 10.751 0.514
Shox2 327 10.349 0.509
ISX 292 10.152 0.509
Sox5 734 9.975 0.545
RAX2 304 9.202 0.508
TLX2 330 8.461 0.509
LHX9 452 8.003 0.510
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (20782 x2 anchors)
CTCF(+) RAD21(-)  904 (4.35%) LA
 959 (4.61%) RA
 45 (0.22%) LA & RA
CTCF(-) RAD21(+)  636 (3.06%) LA
 620 (2.98%) RA
 27 (0.13%) LA & RA
CTCF(+) RAD21(+)  5373 (25.85%) LA
 5402 (25.99%) RA
 1819 (8.75%) LA + RA
CTCF directionality
(20801 cases)		  1733 (8.33%)Convergent ≫ ≪
 65 (0.31%)Divergent ≪ ≫
 660 (3.17%)Tandem ≫ ≫
 7760 (37.31%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF3028171.0810.626
ZBTB22411119.9440.611
Sox5297841.0950.564
FOXL1192335.0240.531
FOXG1128832.0210.529
FOXI1184331.5580.533
FOXO4184331.5580.532
FOXO6184331.5580.531
FOXP3184331.5580.528
MEIS1199828.4200.520
 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