Information
Accession GMS-64-16 (FID: 577)Browse (ALL)
Title Hi-C on HAP-1
HiC file 4DNFI1E6NJQJ (5.03 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-31 10:12:00
Last update date2025-01-31 10:12:00
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 2025-01-31 10:12:00
Reference hg38 (Human)  
Result file DomainCall.tar.gz (309.46 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 6527 domains
11371 boundaries
GMS Loop 11170 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (11371)
CTCF(+) RAD21(-)  388 (3.41%)
CTCF(-) RAD21(+)  369 (3.25%)
CTCF(+) RAD21(+)  1571 (13.82%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5 778 24.475 0.559
RHOXF1 477 20.414 0.522
ZNF354C 508 18.153 0.467
CTCF 269 14.382 0.538
MEIS1 967 14.364 0.510
FOXL1 472 13.297 0.522
ZBTB2 260 13.132 0.537
FOXO4 445 12.353 0.526
FOXP3 445 12.353 0.522
FOXI1 445 12.200 0.528
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (11170 x2 anchors)
CTCF(+) RAD21(-)  407 (3.64%) LA
 447 (4%) RA
 30 (0.27%) LA & RA
CTCF(-) RAD21(+)  357 (3.2%) LA
 349 (3.12%) RA
 17 (0.15%) LA & RA
CTCF(+) RAD21(+)  2933 (26.26%) LA
 2954 (26.45%) RA
 1080 (9.67%) LA + RA
CTCF directionality
(11188 cases)		  958 (8.56%)Convergent ≫ ≪
 46 (0.41%)Divergent ≪ ≫
 393 (3.51%)Tandem ≫ ≫
 3983 (35.6%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF1420124.7470.612
ZBTB2109981.7510.601
FOXL1127846.0320.538
MEIS1137244.2570.522
FOXP3122644.0150.529
FOXI1122543.9220.533
FOXO4122543.6060.533
FOXO6122543.6060.532
RHOXF1107138.4140.516
ZNF354C125236.0720.496
 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