Information
Accession GMS-65-98 (FID: 550)Browse (ALL)
Title Hi-C on sync. HeLa cells - Rep2
HiC file 4DNFIY3KDHP6 (1.21 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-18 09:20:02
Last update date2025-01-18 09:20:02
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 09:20:02
Reference hg38 (Human)  
Result file DomainCall.tar.gz (203.87 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 765 domains
1499 boundaries
GMS Loop 2320 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (1499)
CTCF(+) RAD21(-)  59 (3.94%)
CTCF(-) RAD21(+)  39 (2.6%)
CTCF(+) RAD21(+)  181 (12.07%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
RHOXF1 62 6.385 0.523
ZNF354C 110 5.671 0.462
HOXC4 53 4.142 0.509
CTCF 34 4.103 0.528
Stat5a 32 3.507 0.512
NR2C1 44 3.398 0.496
MEIS1 115 3.220 0.500
POU5F1B 82 3.208 0.510
POU3F4 82 3.147 0.509
MEIS2 51 3.139 0.509
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (2320 x2 anchors)
CTCF(+) RAD21(-)  115 (4.96%) LA
 107 (4.61%) RA
 8 (0.34%) LA & RA
CTCF(-) RAD21(+)  63 (2.72%) LA
 55 (2.37%) RA
 1 (0.04%) LA & RA
CTCF(+) RAD21(+)  326 (14.05%) LA
 344 (14.83%) RA
 64 (2.76%) LA + RA
CTCF directionality
(2320 cases)		  69 (2.97%)Convergent ≫ ≪
 7 (0.3%)Divergent ≪ ≫
 44 (1.9%)Tandem ≫ ≫
 652 (28.1%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Arid3a22227.9590.585
Nr2e327325.8420.512
ZNF518A37025.3000.540
NFATC219325.2800.579
RHOXF123624.5720.539
FOXL126321.2810.525
Foxj219519.8880.514
FOXI124819.4780.529
FOXO424819.4780.526
FOXO624819.4780.526
 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