Information
Accession GMS-65-68 (FID: 520)Browse (ALL)
Title Hi-C on sync. HeLa cells - Rep3
HiC file 4DNFIYJ4TWB8 (1.41 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-17 20:56:40
Last update date2025-01-17 20:56:40
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 2025-01-17 20:56:40
Reference hg38 (Human)  
Result file DomainCall.tar.gz (206.68 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 1029 domains
1978 boundaries
GMS Loop 2538 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (1978)
CTCF(+) RAD21(-)  57 (2.88%)
CTCF(-) RAD21(+)  52 (2.63%)
CTCF(+) RAD21(+)  232 (11.73%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB2 50 6.518 0.537
GSX2 45 4.664 0.518
PDX1 46 4.386 0.511
EMX1 58 4.325 0.509
CTCF 42 4.163 0.536
HOXB2 42 4.086 0.509
VAX2 51 3.087 0.512
HOXB5 55 3.017 0.519
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (2538 x2 anchors)
CTCF(+) RAD21(-)  96 (3.78%) LA
 108 (4.26%) RA
 8 (0.32%) LA & RA
CTCF(-) RAD21(+)  74 (2.92%) LA
 86 (3.39%) RA
 2 (0.08%) LA & RA
CTCF(+) RAD21(+)  392 (15.45%) LA
 380 (14.97%) RA
 63 (2.48%) LA + RA
CTCF directionality
(2538 cases)		  53 (2.09%)Convergent ≫ ≪
 9 (0.35%)Divergent ≪ ≫
 42 (1.65%)Tandem ≫ ≫
 768 (30.26%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox544435.0790.575
ZNF354C30523.8590.462
MEIS129219.8440.512
FOXL127319.1390.533
FOXI126218.4070.531
FOXO426218.4070.528
FOXO626218.4070.526
FOXP326218.4070.523
ISX16718.3480.505
NFATC218317.3750.564
 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