Information
Accession GMS-65-23 (FID: 469)Browse (ALL)
Title Liquified Chromatin Hi-C on K562 cells
HiC file 4DNFIJBJ6QVH (5.35 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-16 11:43:59
Last update date2025-01-16 11:43:59
Contact GMSuite GENOMEMODALITY
gmsuite 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 2025-01-16 11:44:00
Reference hg38 (Human)  
Result file DomainCall.tar.gz (249.15 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3449 domains
6289 boundaries
GMS Loop 4522 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (6289)
CTCF(+) RAD21(-)  227 (3.61%)
CTCF(-) RAD21(+)  185 (2.94%)
CTCF(+) RAD21(+)  872 (13.87%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
MEIS1 351 19.270 0.509
RHOXF1 246 18.582 0.513
NFATC2 200 17.403 0.562
NKX6-1 280 15.910 0.506
HOXD4 204 14.621 0.515
HOXB4 203 14.427 0.509
FOXL1 281 13.849 0.522
CTCF 161 13.580 0.540
Nr2e3 270 13.052 0.508
Foxj2 285 12.583 0.512
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (4522 x2 anchors)
CTCF(+) RAD21(-)  186 (4.11%) LA
 176 (3.89%) RA
 15 (0.33%) LA & RA
CTCF(-) RAD21(+)  144 (3.18%) LA
 152 (3.36%) RA
 7 (0.15%) LA & RA
CTCF(+) RAD21(+)  735 (16.25%) LA
 744 (16.45%) RA
 184 (4.07%) LA + RA
CTCF directionality
(4522 cases)		  141 (3.12%)Convergent ≫ ≪
 24 (0.53%)Divergent ≪ ≫
 95 (2.1%)Tandem ≫ ≫
 1321 (29.21%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Nr2e352041.0420.515
MEIS195040.2590.501
FOXL153732.9610.524
FOXI150328.7070.528
FOXO450328.7070.520
FOXP350328.7070.519
FOXO650328.4920.525
Sox529927.5720.552
ZBTB227724.4540.537
HOXB430722.7890.502
 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