Information
Accession GMS-64-19 (FID: 583)Browse (ALL)
Title Hi-C on HAP-1 +/- WAPL or SCC4 KO
HiC file 4DNFI4SNMW2H (4.76 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-31 22:59:28
Last update date2025-01-31 22:59:28
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 22:59:29
Reference hg38 (Human)  
Result file DomainCall.tar.gz (337.60 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 6918 domains
11634 boundaries
GMS Loop 18294 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (11634)
CTCF(+) RAD21(-)  372 (3.2%)
CTCF(-) RAD21(+)  418 (3.59%)
CTCF(+) RAD21(+)  1951 (16.77%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 485 50.419 0.566
ZBTB2 438 41.455 0.558
MEIS1 532 17.361 0.510
Nr2e3 448 14.833 0.500
Sox5 672 14.242 0.538
ZNF354C 479 12.257 0.522
Arid3a 330 11.905 0.547
FOXL1 432 11.800 0.516
FOXP3 411 11.062 0.520
FOXO4 409 10.862 0.522
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (18294 x2 anchors)
CTCF(+) RAD21(-)  689 (3.77%) LA
 667 (3.65%) RA
 28 (0.15%) LA & RA
CTCF(-) RAD21(+)  564 (3.08%) LA
 616 (3.37%) RA
 30 (0.16%) LA & RA
CTCF(+) RAD21(+)  4243 (23.19%) LA
 4283 (23.41%) RA
 1240 (6.78%) LA + RA
CTCF directionality
(18310 cases)		  957 (5.23%)Convergent ≫ ≪
 77 (0.42%)Divergent ≪ ≫
 624 (3.41%)Tandem ≫ ≫
 6598 (36.03%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF2214126.0850.606
ZBTB22000106.9300.592
Sox5252341.0430.553
MEIS1317328.2070.521
LHX5164725.4360.517
FOXL1158523.8210.522
NKX6-1155523.8130.513
FOXP3152223.1560.521
FOXI1151623.1050.532
FOXO4151623.1050.524
 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