Information
Accession GMS-64-27 (FID: 593)Browse (ALL)
Title Hi-C on RAD21-AID tagged HCT-116
HiC file 4DNFIBCIA62Q (5.92 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-04 14:00:18
Last update date2025-02-04 14:00:18
Contact Sung-Joon PARK
park AT hgc.jp
The University of Tokyo
Sharingopen access
Keywords Hi-C  4DN  contact matrix 
 Domain/Loop Calling Information

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Submit date 2025-02-04 14:00:18
Reference hg38 (Human)  
Result file DomainCall.tar.gz (198.17 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 1303 domains
2460 boundaries
GMS Loop 1862 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (2460)
CTCF(+) RAD21(-)  104 (4.23%)
CTCF(-) RAD21(+)  70 (2.85%)
CTCF(+) RAD21(+)  276 (11.22%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5 167 10.037 0.567
FOXG1 66 8.733 0.514
RHOXF1 96 7.900 0.518
FOXO3 111 7.453 0.512
FOXL1 105 7.173 0.510
GATA3 111 6.665 0.501
ZNF354C 116 6.612 0.446
FOXO4 99 6.376 0.521
FOXO6 99 6.376 0.520
FOXP3 99 6.376 0.518
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (1862 x2 anchors)
CTCF(+) RAD21(-)  68 (3.65%) LA
 61 (3.28%) RA
 9 (0.48%) LA & RA
CTCF(-) RAD21(+)  57 (3.06%) LA
 44 (2.36%) RA
 5 (0.27%) LA & RA
CTCF(+) RAD21(+)  364 (19.55%) LA
 358 (19.23%) RA
 154 (8.27%) LA + RA
CTCF directionality
(1862 cases)		  39 (2.09%)Convergent ≫ ≪
 13 (0.7%)Divergent ≪ ≫
 135 (7.25%)Tandem ≫ ≫
 477 (25.62%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CENPB28745.2990.532
Arid3a17929.8920.510
NFATC214620.6510.539
Sox511619.3470.522
MEIS122017.6710.505
FOXL119315.9840.503
FOXI117714.0430.513
FOXO417714.0430.511
FOXO617714.0430.512
FOXP317714.0430.508
 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