Information
Accession GMS-65-9 (FID: 455)Browse (ALL)
Title Hi-C on K562
HiC file 4DNFITUOMFUQ (6.73 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-16 11:19:07
Last update date2025-01-16 11:19:07
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 11:19:08
Reference hg38 (Human)  
Result file DomainCall.tar.gz (303.26 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 5819 domains
10162 boundaries
GMS Loop 9936 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (10162)
CTCF(+) RAD21(-)  321 (3.16%)
CTCF(-) RAD21(+)  362 (3.56%)
CTCF(+) RAD21(+)  1550 (15.25%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5 786 35.832 0.567
RHOXF1 479 29.666 0.520
MEIS1 973 24.266 0.504
Nr2e3 456 23.534 0.512
ZBTB2 280 20.139 0.542
RAX2 308 19.689 0.501
ISX 279 18.614 0.499
TEAD3 281 18.159 0.496
Shox2 284 18.130 0.500
VAX1 365 18.119 0.496
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (9936 x2 anchors)
CTCF(+) RAD21(-)  438 (4.41%) LA
 425 (4.28%) RA
 24 (0.24%) LA & RA
CTCF(-) RAD21(+)  317 (3.19%) LA
 335 (3.37%) RA
 17 (0.17%) LA & RA
CTCF(+) RAD21(+)  2475 (24.91%) LA
 2564 (25.81%) RA
 813 (8.18%) LA + RA
CTCF directionality
(9945 cases)		  722 (7.26%)Convergent ≫ ≪
 41 (0.41%)Divergent ≪ ≫
 324 (3.26%)Tandem ≫ ≫
 3746 (37.67%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF1336132.6830.606
ZBTB2109796.7000.592
Sox5188480.2250.583
FOXL1121449.5100.529
Nr2e3114548.3700.512
FOXI1116046.4190.534
FOXO4116046.4190.532
FOXO6116046.4190.532
FOXP3116346.4160.527
GATA3115239.1160.499
 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