Information
Accession GMS-64-76 (FID: 665)Browse (ALL)
Title in situ Hi-C on an allelic series of iPSCs differentiated to cardiac cells
HiC file 4DNFIPVMIIRE (8.82 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-18 15:29:25
Last update date2025-02-18 15:29:25
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 15:29:26
Reference hg38 (Human)  
Result file DomainCall.tar.gz (447.77 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 11003 domains
18463 boundaries
GMS Loop 28672 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (18463)
CTCF(+) RAD21(-)  630 (3.41%)
CTCF(-) RAD21(+)  554 (3%)
CTCF(+) RAD21(+)  2691 (14.58%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 564 31.051 0.550
ZBTB2 485 21.930 0.540
Sox5 1113 19.455 0.545
MEIS1 853 17.682 0.511
RHOXF1 591 13.248 0.512
Nr2e3 671 11.862 0.502
FOXL1 696 11.480 0.511
NFATC2 451 10.962 0.539
FOXI1 656 10.209 0.516
FOXO4 656 10.058 0.514
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (28672 x2 anchors)
CTCF(+) RAD21(-)  1323 (4.61%) LA
 1361 (4.75%) RA
 97 (0.34%) LA & RA
CTCF(-) RAD21(+)  888 (3.1%) LA
 837 (2.92%) RA
 42 (0.15%) LA & RA
CTCF(+) RAD21(+)  7813 (27.25%) LA
 7899 (27.55%) RA
 2883 (10.06%) LA + RA
CTCF directionality
(28739 cases)		  2595 (9.03%)Convergent ≫ ≪
 110 (0.38%)Divergent ≪ ≫
 1143 (3.98%)Tandem ≫ ≫
 10834 (37.7%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF4119173.7070.630
ZBTB23209117.4870.616
FOXL1306246.9660.532
FOXO4291544.7450.534
FOXO6291544.7450.533
FOXP3291544.7450.529
FOXI1291744.4800.536
MEIS1325042.8800.515
Arid3a237541.6180.546
ZNF354C304735.5690.478
 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