Information
Accession GMS-64-69 (FID: 654)Browse (ALL)
Title in situ Hi-C on primary human cardiomyocytes
HiC file 4DNFI6T12WJF (5.28 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-18 15:16:30
Last update date2025-02-18 15:16:30
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 15:16:31
Reference hg38 (Human)  
Result file DomainCall.tar.gz (289.08 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 4932 domains
9091 boundaries
GMS Loop 9173 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (9091)
CTCF(+) RAD21(-)  296 (3.26%)
CTCF(-) RAD21(+)  266 (2.93%)
CTCF(+) RAD21(+)  1136 (12.5%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB2 249 18.973 0.538
CTCF 241 17.543 0.540
ZNF354C 706 15.807 0.529
RHOXF1 310 11.738 0.519
VAX1 286 11.519 0.500
MEIS1 366 10.797 0.505
HOXB5 263 10.627 0.513
EMX1 268 10.469 0.504
VAX2 207 9.369 0.503
VSX1 358 8.802 0.503
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (9173 x2 anchors)
CTCF(+) RAD21(-)  370 (4.03%) LA
 358 (3.9%) RA
 18 (0.2%) LA & RA
CTCF(-) RAD21(+)  268 (2.92%) LA
 311 (3.39%) RA
 14 (0.15%) LA & RA
CTCF(+) RAD21(+)  2065 (22.51%) LA
 2093 (22.82%) RA
 618 (6.74%) LA + RA
CTCF directionality
(9177 cases)		  525 (5.72%)Convergent ≫ ≪
 27 (0.29%)Divergent ≪ ≫
 276 (3.01%)Tandem ≫ ≫
 3238 (35.28%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF91279.4130.590
ZBTB289076.1210.579
Sox5163563.3930.581
FOXL1107847.1160.532
RHOXF1100044.1060.521
FOXI1102443.6370.541
FOXO4102443.6370.539
FOXO6102443.6370.539
FOXP3102443.6370.534
MEIS1116839.3850.520
 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