Information
Accession GMS-65-69 (FID: 521)Browse (ALL)
Title Hi-C on HeLa cells - protocol variations
HiC file 4DNFIBY3UHJB (2.23 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-17 20:57:00
Last update date2025-01-17 20:57:00
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 20:57:00
Reference hg38 (Human)  
Result file DomainCall.tar.gz (246.00 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 2471 domains
4749 boundaries
GMS Loop 4899 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (4749)
CTCF(+) RAD21(-)  167 (3.52%)
CTCF(-) RAD21(+)  161 (3.39%)
CTCF(+) RAD21(+)  642 (13.52%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
FOXL1 209 14.659 0.525
FOXP3 199 14.168 0.528
FOXI1 198 13.961 0.533
FOXO4 198 13.961 0.532
FOXO6 198 13.961 0.531
ZBTB2 126 12.770 0.540
Sox5 305 12.701 0.553
NFATC2 128 12.331 0.557
RHOXF1 201 11.256 0.522
GATA3 233 10.662 0.516
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (4899 x2 anchors)
CTCF(+) RAD21(-)  206 (4.2%) LA
 195 (3.98%) RA
 13 (0.27%) LA & RA
CTCF(-) RAD21(+)  124 (2.53%) LA
 158 (3.23%) RA
 6 (0.12%) LA & RA
CTCF(+) RAD21(+)  809 (16.51%) LA
 932 (19.02%) RA
 206 (4.2%) LA + RA
CTCF directionality
(4899 cases)		  170 (3.47%)Convergent ≫ ≪
 21 (0.43%)Divergent ≪ ≫
 117 (2.39%)Tandem ≫ ≫
 1526 (31.15%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox590753.4990.571
ZNF354C60149.4030.425
CTCF39945.2550.548
ZNF518A81638.6880.539
RHOXF153137.5580.524
FOXL156635.1870.528
MEIS161634.4330.502
FOXI153731.9330.533
FOXO453731.9330.524
FOXP353731.9330.525
 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