Information
Accession GMS-64-32 (FID: 599)Browse (ALL)
Title Hi-C on RAD21-AID tagged HCT-116
HiC file 4DNFIP71EWXC (18.07 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-04 14:18:36
Last update date2025-02-04 14:18:36
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 14:18:36
Reference hg38 (Human)  
Result file DomainCall.tar.gz (296.79 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 7027 domains
11849 boundaries
GMS Loop 9230 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (11849)
CTCF(+) RAD21(-)  381 (3.22%)
CTCF(-) RAD21(+)  357 (3.01%)
CTCF(+) RAD21(+)  1744 (14.72%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5 819 31.299 0.566
CTCF 375 29.180 0.541
FOXL1 538 27.549 0.520
MEIS1 612 26.517 0.504
ZNF518A 765 25.100 0.523
FOXI1 501 23.933 0.533
FOXO4 501 23.933 0.526
FOXO6 501 23.933 0.526
FOXP3 501 23.933 0.526
RHOXF1 515 22.371 0.520
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (9230 x2 anchors)
CTCF(+) RAD21(-)  340 (3.68%) LA
 302 (3.27%) RA
 17 (0.18%) LA & RA
CTCF(-) RAD21(+)  312 (3.38%) LA
 275 (2.98%) RA
 13 (0.14%) LA & RA
CTCF(+) RAD21(+)  2211 (23.95%) LA
 2348 (25.44%) RA
 883 (9.57%) LA + RA
CTCF directionality
(9235 cases)		  594 (6.43%)Convergent ≫ ≪
 34 (0.37%)Divergent ≪ ≫
 458 (4.96%)Tandem ≫ ≫
 3039 (32.91%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF84769.1140.601
ZBTB279361.3560.593
Sox5140448.7540.534
ZNF354C304836.9420.491
FOXL194436.5720.524
LHX590233.9320.485
FOXO689833.2420.517
FOXP390033.1680.514
FOXI189733.1400.517
FOXO489733.1400.516
 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