Information
Accession GMS-64-30 (FID: 597)Browse (ALL)
Title Hi-C on RAD21-AID tagged HCT-116
HiC file 4DNFI7XAZNNQ (5.45 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-04 14:11:14
Last update date2025-02-04 14:11:14
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 2025-02-04 14:11:15
Reference hg38 (Human)  
Result file DomainCall.tar.gz (260.86 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3667 domains
6665 boundaries
GMS Loop 6840 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (6665)
CTCF(+) RAD21(-)  238 (3.57%)
CTCF(-) RAD21(+)  202 (3.03%)
CTCF(+) RAD21(+)  965 (14.48%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C 604 20.560 0.505
CTCF 196 19.435 0.536
MEIS1 330 18.508 0.498
Nr2e3 277 18.038 0.512
ZBTB2 181 16.141 0.534
FOXL1 294 14.251 0.516
RHOXF1 272 13.693 0.520
FOXP3 282 13.231 0.518
FOXI1 282 13.088 0.526
FOXO4 281 13.075 0.524
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (6840 x2 anchors)
CTCF(+) RAD21(-)  286 (4.18%) LA
 285 (4.17%) RA
 21 (0.31%) LA & RA
CTCF(-) RAD21(+)  217 (3.17%) LA
 206 (3.01%) RA
 9 (0.13%) LA & RA
CTCF(+) RAD21(+)  1752 (25.61%) LA
 1795 (26.24%) RA
 630 (9.21%) LA + RA
CTCF directionality
(6846 cases)		  561 (8.19%)Convergent ≫ ≪
 35 (0.51%)Divergent ≪ ≫
 231 (3.37%)Tandem ≫ ≫
 2476 (36.17%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF837103.4010.606
ZBTB263965.5000.593
MEIS1151649.1380.510
RHOXF180649.0560.524
FOXL183645.0470.523
FOXP380543.1200.522
FOXI180043.0160.531
FOXO480043.0160.521
FOXO680043.0160.529
Nr2e381440.9360.508
 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