Information
Accession GMS-64-77 (FID: 666)Browse (ALL)
Title in situ Hi-C on an allelic series of iPSCs differentiated to cardiac cells
HiC file 4DNFIPTFHCFP (8.43 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-18 15:29:31
Last update date2025-02-18 15:29:31
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 15:29:31
Reference hg38 (Human)  
Result file DomainCall.tar.gz (454.79 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 11025 domains
18606 boundaries
GMS Loop 31072 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (18606)
CTCF(+) RAD21(-)  597 (3.21%)
CTCF(-) RAD21(+)  652 (3.5%)
CTCF(+) RAD21(+)  2806 (15.08%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 655 41.934 0.553
ZBTB2 524 25.915 0.548
Sox5 1146 18.409 0.548
NFATC2 440 13.483 0.543
RHOXF1 590 11.383 0.512
LHX5 389 11.276 0.506
LMX1A 367 10.048 0.507
Nr2e3 680 9.661 0.515
UNCX 384 9.355 0.511
MEIS1 618 8.672 0.505
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (31072 x2 anchors)
CTCF(+) RAD21(-)  1444 (4.65%) LA
 1449 (4.66%) RA
 105 (0.34%) LA & RA
CTCF(-) RAD21(+)  1101 (3.54%) LA
 1086 (3.5%) RA
 57 (0.18%) LA & RA
CTCF(+) RAD21(+)  9672 (31.13%) LA
 9647 (31.05%) RA
 3834 (12.34%) LA + RA
CTCF directionality
(31156 cases)		  3406 (10.93%)Convergent ≫ ≪
 129 (0.41%)Divergent ≪ ≫
 1474 (4.73%)Tandem ≫ ≫
 12362 (39.68%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF4969205.3370.651
ZBTB24248162.3460.631
Sox5498658.1870.563
ZNF354C302837.6150.468
FOXL1323536.2660.524
MEIS1339035.6880.501
FOXO6307534.6450.529
FOXI1307434.6100.529
FOXO4307434.6100.524
FOXP3308934.2340.525
 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