Information
Accession GMS-65-78 (FID: 530)Browse (ALL)
Title Hi-C on ENCODE3 cell lines
HiC file 4DNFICEGAHRC (15.57 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-18 01:53:27
Last update date2025-01-18 01:53:27
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 2025-01-18 01:53:28
Reference hg38 (Human)  
Result file DomainCall.tar.gz (428.44 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 10716 domains
17809 boundaries
GMS Loop 24900 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (17809)
CTCF(+) RAD21(-)  663 (3.72%)
CTCF(-) RAD21(+)  548 (3.08%)
CTCF(+) RAD21(+)  2759 (15.49%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 610 39.195 0.553
ZBTB2 514 27.084 0.550
FOXI1 690 18.128 0.524
FOXO4 690 18.128 0.521
FOXO6 690 18.128 0.521
FOXP3 690 18.128 0.518
FOXL1 734 17.969 0.518
MEIS1 1441 14.958 0.502
Nr2e3 717 13.320 0.511
FOXO3 652 12.417 0.513
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (24900 x2 anchors)
CTCF(+) RAD21(-)  1241 (4.98%) LA
 1237 (4.97%) RA
 82 (0.33%) LA & RA
CTCF(-) RAD21(+)  754 (3.03%) LA
 793 (3.18%) RA
 33 (0.13%) LA & RA
CTCF(+) RAD21(+)  6610 (26.55%) LA
 6765 (27.17%) RA
 2354 (9.45%) LA + RA
CTCF directionality
(24951 cases)		  2071 (8.3%)Convergent ≫ ≪
 108 (0.43%)Divergent ≪ ≫
 1047 (4.2%)Tandem ≫ ≫
 9503 (38.09%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF3570170.6410.627
ZBTB22943126.3710.611
FOXL1265538.2340.521
MEIS1280337.9960.501
FOXP3253735.8970.528
FOXO4252535.3890.526
FOXO6252535.3890.527
FOXI1252435.3470.529
RHOXF1221232.5550.514
ZNF354C237029.5880.479
 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