Information
Accession GMS-64-24 (FID: 589)Browse (ALL)
Title Hi-C on RAD21-AID tagged HCT-116
HiC file 4DNFIQRTP7NM (5.50 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-04 13:59:18
Last update date2025-02-04 13:59:18
Contact Sung-Joon PARK
park AT hgc.jp
The University of Tokyo
Sharingopen access
Keywords Hi-C  4DN  contact matrix 
 Domain/Loop Calling Information

URL copied to the clipboard
Submit date 2025-02-04 13:59:18
Reference hg38 (Human)  
Result file DomainCall.tar.gz (212.30 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 1757 domains
3313 boundaries
GMS Loop 2552 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (3313)
CTCF(+) RAD21(-)  116 (3.5%)
CTCF(-) RAD21(+)  102 (3.08%)
CTCF(+) RAD21(+)  394 (11.89%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5 242 18.910 0.569
FOXO4 317 15.649 0.532
FOXI1 317 15.567 0.537
FOXO6 317 15.567 0.530
ZNF354C 163 12.077 0.503
FOXL1 158 11.589 0.521
MEIS1 300 11.505 0.490
NR2C2(var.2) 100 10.866 0.510
NFATC2 101 10.570 0.566
FOXP3 150 10.441 0.525
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (2552 x2 anchors)
CTCF(+) RAD21(-)  92 (3.61%) LA
 116 (4.55%) RA
 14 (0.55%) LA & RA
CTCF(-) RAD21(+)  67 (2.63%) LA
 67 (2.63%) RA
 11 (0.43%) LA & RA
CTCF(+) RAD21(+)  550 (21.55%) LA
 555 (21.75%) RA
 233 (9.13%) LA + RA
CTCF directionality
(2553 cases)		  95 (3.72%)Convergent ≫ ≪
 19 (0.74%)Divergent ≪ ≫
 172 (6.74%)Tandem ≫ ≫
 743 (29.1%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox547239.2530.542
Arid3a27834.8450.520
MEIS154830.8600.504
Nr2e330929.3850.495
CTCF18927.7330.566
NFATC221125.5770.555
FOXL130420.8120.515
RHOXF124719.4880.491
FOXI128619.2670.520
FOXO628619.2670.520
 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