Information
Accession GMS-65-17 (FID: 463)Browse (ALL)
Title Liquified Chromatin Hi-C on K562 cells
HiC file 4DNFIWNNO89O (3.01 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-16 11:30:56
Last update date2025-01-16 11:30:56
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 11:30:57
Reference hg38 (Human)  
Result file DomainCall.tar.gz (213.08 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 1571 domains
2969 boundaries
GMS Loop 1985 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (2969)
CTCF(+) RAD21(-)  92 (3.1%)
CTCF(-) RAD21(+)  107 (3.6%)
CTCF(+) RAD21(+)  354 (11.92%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5 203 14.178 0.562
Dlx2 97 12.299 0.511
NFATC2 93 11.537 0.557
FOXL1 134 10.709 0.527
Arid3a 108 9.902 0.535
FOXI1 125 9.301 0.531
FOXO4 125 9.301 0.530
FOXO6 125 9.301 0.530
FOXP3 125 9.301 0.526
RHOXF1 127 8.901 0.514
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (1985 x2 anchors)
CTCF(+) RAD21(-)  94 (4.74%) LA
 102 (5.14%) RA
 4 (0.2%) LA & RA
CTCF(-) RAD21(+)  44 (2.22%) LA
 38 (1.91%) RA
 3 (0.15%) LA & RA
CTCF(+) RAD21(+)  328 (16.52%) LA
 351 (17.68%) RA
 80 (4.03%) LA + RA
CTCF directionality
(1985 cases)		  65 (3.27%)Convergent ≫ ≪
 11 (0.55%)Divergent ≪ ≫
 49 (2.47%)Tandem ≫ ≫
 625 (31.49%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C34469.8220.448
Sox545067.0230.571
RHOXF129148.5820.537
MEIS131344.7550.522
NFATC222344.6920.583
FOXL129341.7680.528
FOXI128040.3400.523
FOXO428040.3400.522
FOXO628040.3400.522
FOXP328040.3400.514
 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