Information
Accession GMS-64-20 (FID: 585)Browse (ALL)
Title Hi-C on HAP-1 +/- WAPL or SCC4 KO
HiC file 4DNFI6JJQKFJ (3.82 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-31 10:44:58
Last update date2025-01-31 10:44:58
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 10:44:58
Reference hg38 (Human)  
Result file DomainCall.tar.gz (252.24 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3992 domains
7309 boundaries
GMS Loop 5607 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (7309)
CTCF(+) RAD21(-)  232 (3.17%)
CTCF(-) RAD21(+)  223 (3.05%)
CTCF(+) RAD21(+)  853 (11.67%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF518A 432 12.195 0.531
ZBTB2 167 10.877 0.528
CTCF 162 10.008 0.529
Sox5 435 9.586 0.553
ZNF354C 248 8.844 0.457
FOXL1 264 8.459 0.525
Nobox 186 7.964 0.518
FOXI1 250 7.894 0.526
FOXO4 250 7.894 0.524
FOXO6 250 7.894 0.523
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (5607 x2 anchors)
CTCF(+) RAD21(-)  193 (3.44%) LA
 221 (3.94%) RA
 12 (0.21%) LA & RA
CTCF(-) RAD21(+)  167 (2.98%) LA
 144 (2.57%) RA
 5 (0.09%) LA & RA
CTCF(+) RAD21(+)  1073 (19.14%) LA
 1057 (18.85%) RA
 299 (5.33%) LA + RA
CTCF directionality
(5607 cases)		  238 (4.24%)Convergent ≫ ≪
 17 (0.3%)Divergent ≪ ≫
 149 (2.66%)Tandem ≫ ≫
 1736 (30.96%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF56469.8030.571
ZBTB239034.8820.563
MEIS159120.0080.508
NFATC231218.1090.544
FOXL149918.0000.521
FOXI147817.3350.524
FOXO447817.3350.522
FOXO647817.3350.522
FOXP347817.3350.519
NKX6-145916.3600.509
 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