Information
Accession GMS-64-52 (FID: 624)Browse (ALL)
Title in situ Hi-C on primary human cardiomyocytes
HiC file 4DNFI8EU526N (9.32 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-08 13:02:05
Last update date2025-02-08 13:02:05
Contact Sung-Joon PARK
park AT hgc.jp
The University of Tokyo
Sharingopen access
Keywords Hi-C  4DN  contact matrix 
 Domain/Loop Calling Information

URL copied to the clipboard
Submit date 2025-02-08 13:02:07
Reference hg38 (Human)  
Result file DomainCall.tar.gz (311.83 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 6485 domains
11492 boundaries
GMS Loop 11232 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (11492)
CTCF(+) RAD21(-)  335 (2.92%)
CTCF(-) RAD21(+)  439 (3.82%)
CTCF(+) RAD21(+)  1662 (14.46%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 336 24.215 0.534
ZBTB2 311 20.228 0.536
Sox5 731 13.179 0.556
NFATC2 306 10.820 0.550
Arid3a 361 9.954 0.545
Msx3 232 9.235 0.503
Nobox 295 8.766 0.511
Nr2e3 417 8.710 0.514
MSX2 354 8.400 0.500
LHX9 409 7.654 0.502
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (11232 x2 anchors)
CTCF(+) RAD21(-)  398 (3.54%) LA
 407 (3.62%) RA
 19 (0.17%) LA & RA
CTCF(-) RAD21(+)  422 (3.76%) LA
 433 (3.86%) RA
 22 (0.2%) LA & RA
CTCF(+) RAD21(+)  2852 (25.39%) LA
 2892 (25.75%) RA
 923 (8.22%) LA + RA
CTCF directionality
(11248 cases)		  789 (7.01%)Convergent ≫ ≪
 45 (0.4%)Divergent ≪ ≫
 350 (3.11%)Tandem ≫ ≫
 4213 (37.46%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF1601149.1900.606
ZBTB21248100.4980.598
ZNF354C267079.6640.451
Sox5207274.5360.578
MEIS1156952.4360.531
RHOXF1124551.9890.523
FOXL1137347.0330.533
FOXI1130842.6540.536
FOXO4130842.6540.535
FOXO6130842.6540.533
 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