Information
Accession GMS-64-49 (FID: 619)Browse (ALL)
Title in situ Hi-C on primary human cardiomyocytes
HiC file 4DNFI9FI1WN4 (6.22 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-08 12:49:03
Last update date2025-02-08 12:49:03
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 2025-02-08 12:49:03
Reference hg38 (Human)  
Result file DomainCall.tar.gz (308.62 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 5996 domains
10720 boundaries
GMS Loop 11135 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (10720)
CTCF(+) RAD21(-)  384 (3.58%)
CTCF(-) RAD21(+)  330 (3.08%)
CTCF(+) RAD21(+)  1516 (14.14%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 338 27.892 0.539
ZBTB2 315 23.860 0.536
Sox5 647 17.990 0.553
FOXL1 422 16.184 0.510
FOXP3 404 15.609 0.519
FOXI1 402 15.362 0.525
FOXO4 402 15.362 0.517
FOXO6 402 15.362 0.522
RHOXF1 407 14.194 0.519
FOXG1 303 13.496 0.516
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (11135 x2 anchors)
CTCF(+) RAD21(-)  462 (4.15%) LA
 429 (3.85%) RA
 27 (0.24%) LA & RA
CTCF(-) RAD21(+)  333 (2.99%) LA
 345 (3.1%) RA
 18 (0.16%) LA & RA
CTCF(+) RAD21(+)  2650 (23.8%) LA
 2618 (23.51%) RA
 826 (7.42%) LA + RA
CTCF directionality
(11145 cases)		  729 (6.54%)Convergent ≫ ≪
 39 (0.35%)Divergent ≪ ≫
 333 (2.99%)Tandem ≫ ≫
 3977 (35.68%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF1649157.8230.604
ZBTB2112585.5020.592
MEIS1238250.5900.517
RHOXF198442.0560.526
ZNF354C121141.3930.488
FOXL1122039.2230.527
FOXP3117338.2540.526
FOXO4116637.6290.530
FOXO6116637.6290.530
FOXI1116637.3380.534
 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