Information
Accession GMS-65-47 (FID: 494)Browse (ALL)
Title Hi-C on GM12878 cells - protocol variations
HiC file 4DNFI9ZWZ5BS (3.55 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-17 10:06:15
Last update date2025-01-17 10:06:15
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 10:06:18
Reference hg38 (Human)  
Result file DomainCall.tar.gz (308.74 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 4627 domains
8534 boundaries
GMS Loop 9143 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (8534)
CTCF(+) RAD21(-)  318 (3.73%)
CTCF(-) RAD21(+)  271 (3.18%)
CTCF(+) RAD21(+)  1137 (13.32%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5 599 24.779 0.569
CTCF 234 18.515 0.537
ZNF518A 578 18.266 0.535
MEIS1 421 16.879 0.498
FOXL1 368 13.661 0.521
RHOXF1 339 13.486 0.525
FOXP3 350 13.410 0.524
FOXI1 348 13.147 0.527
FOXO4 348 13.147 0.523
FOXO6 348 12.997 0.523
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (9143 x2 anchors)
CTCF(+) RAD21(-)  396 (4.33%) LA
 411 (4.5%) RA
 27 (0.3%) LA & RA
CTCF(-) RAD21(+)  269 (2.94%) LA
 259 (2.83%) RA
 14 (0.15%) LA & RA
CTCF(+) RAD21(+)  2139 (23.39%) LA
 2192 (23.97%) RA
 698 (7.63%) LA + RA
CTCF directionality
(9146 cases)		  616 (6.74%)Convergent ≫ ≪
 42 (0.46%)Divergent ≪ ≫
 291 (3.18%)Tandem ≫ ≫
 3246 (35.49%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF101996.2320.591
Sox5162263.3780.576
ZBTB275757.1590.581
MEIS1120345.4780.500
RHOXF194345.1210.533
FOXL1105841.9410.530
FOXP3101039.1770.525
FOXO4100738.8620.532
FOXO6100738.8620.531
FOXI1100638.7570.534
 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