Information
Accession GMS-64-49 (FID: 618)Browse (ALL)
Title in situ Hi-C on primary human cardiomyocytes
HiC file 4DNFIQ4QM36P (5.76 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

URL copied to the clipboard
Submit date 2025-02-08 12:49:03
Reference hg38 (Human)  
Result file DomainCall.tar.gz (305.24 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 5944 domains
10696 boundaries
GMS Loop 10619 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (10696)
CTCF(+) RAD21(-)  398 (3.72%)
CTCF(-) RAD21(+)  312 (2.92%)
CTCF(+) RAD21(+)  1505 (14.07%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 329 26.401 0.546
ZBTB2 323 25.347 0.540
Sox5 646 17.139 0.557
MEIS1 490 16.388 0.507
FOXI1 398 15.515 0.523
FOXO4 398 15.515 0.520
FOXO6 398 15.515 0.518
FOXP3 398 15.515 0.515
FOXL1 414 15.482 0.513
RHOXF1 338 13.045 0.519
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (10619 x2 anchors)
CTCF(+) RAD21(-)  501 (4.72%) LA
 502 (4.73%) RA
 27 (0.25%) LA & RA
CTCF(-) RAD21(+)  293 (2.76%) LA
 288 (2.71%) RA
 8 (0.08%) LA & RA
CTCF(+) RAD21(+)  2595 (24.44%) LA
 2612 (24.6%) RA
 813 (7.66%) LA + RA
CTCF directionality
(10633 cases)		  745 (7.01%)Convergent ≫ ≪
 36 (0.34%)Divergent ≪ ≫
 346 (3.25%)Tandem ≫ ≫
 3984 (37.47%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF1360124.8220.607
ZBTB2114994.9740.588
ZNF518A158845.2990.534
MEIS1122540.3910.512
RHOXF1104540.2260.514
Arid3a91139.7770.527
FOXL1115837.6760.541
FOXI1110935.2040.538
FOXO4110935.2040.536
FOXO6110935.2040.537
 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