Information
Accession GMS-65-70 (FID: 522)Browse (ALL)
Title Hi-C on HeLa cells - protocol variations
HiC file 4DNFIOUSETUP (1.63 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-17 20:58:20
Last update date2025-01-17 20:58:20
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 20:58:20
Reference hg38 (Human)  
Result file DomainCall.tar.gz (261.72 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3170 domains
6049 boundaries
GMS Loop 6713 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (6049)
CTCF(+) RAD21(-)  204 (3.37%)
CTCF(-) RAD21(+)  179 (2.96%)
CTCF(+) RAD21(+)  907 (14.99%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 220 29.219 0.545
ZBTB2 213 27.349 0.542
Sox5 391 17.368 0.550
MEIS1 270 12.452 0.510
Arid3a 186 11.699 0.566
ZNF354C 230 10.939 0.480
RHOXF1 206 10.834 0.514
Nr2e3 227 10.337 0.512
NFATC2 152 8.734 0.549
FOXL1 236 8.704 0.524
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (6713 x2 anchors)
CTCF(+) RAD21(-)  259 (3.86%) LA
 280 (4.17%) RA
 26 (0.39%) LA & RA
CTCF(-) RAD21(+)  201 (2.99%) LA
 223 (3.32%) RA
 7 (0.1%) LA & RA
CTCF(+) RAD21(+)  1237 (18.43%) LA
 1241 (18.49%) RA
 305 (4.54%) LA + RA
CTCF directionality
(6713 cases)		  253 (3.77%)Convergent ≫ ≪
 25 (0.37%)Divergent ≪ ≫
 161 (2.4%)Tandem ≫ ≫
 2139 (31.86%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF53648.7630.565
ZBTB246636.9880.555
FOXL172131.1140.528
MEIS159330.1090.511
FOXI168229.2030.535
FOXO668229.2030.533
FOXO468129.0800.534
FOXP368129.0800.529
Foxj251522.9340.514
VSX243121.4650.503
 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