Information
Accession GMS-64-61 (FID: 643)Browse (ALL)
Title Hi-C on mouse cerebellar granule neurons
HiC file 4DNFI1HWXE8A (2.46 GB)
 hic mCool Cooler-Tree
Submit date2025-02-11 11:17:16
Last update date2025-02-11 11:17:16
Contact Sung-Joon PARK
park 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 2025-02-11 11:17:16
Reference mm10 (Mouse)  
Result file DomainCall.tar.gz (275.74 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3833 domains
7078 boundaries
GMS Loop 10810 loops
 Hi-C map is too sparse
Motifs in 5Kb Boundaries (7078)
CTCF(+) RAD21(-)  160 (2.26%)
CTCF(-) RAD21(+)  165 (2.33%)
CTCF(+) RAD21(+)  1183 (16.71%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue
ROC
AUC
ZNF354C 1426 21.567 0.560
CTCF 207 19.755 0.556
ZBTB2 163 10.943 0.550
ZNF518A 825 7.849 0.520
VSX1 227 7.368 0.509
FOXD1 293 6.878 0.524
LHX9 283 6.834 0.497
PRRX1 298 6.764 0.501
PRRX2 283 6.741 0.500
LBX1 269 6.645 0.501
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (10810 x2 anchors)
CTCF(+) RAD21(-)  244 (2.26%) LA
 294 (2.72%) RA
 7 (0.06%) LA & RA
CTCF(-) RAD21(+)  341 (3.15%) LA
 357 (3.3%) RA
 6 (0.06%) LA & RA
CTCF(+) RAD21(+)  2671 (24.71%) LA
 2598 (24.03%) RA
 810 (7.49%) LA + RA
CTCF directionality
(10818 cases)
 582 (5.38%)Convergent ≫ ≪
 59 (0.55%)Divergent ≪ ≫
 338 (3.12%)Tandem ≫ ≫
 3865 (35.73%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue
ROC
AUC
CTCF101274.4080.604
ZBTB286655.5190.588
ZNF354C177649.5520.590
NFATC2123039.0410.569
Sox599131.5260.568
GATA3135430.9190.500
LMX1A115829.9850.513
Lhx4100726.5560.505
Nr2e385126.4240.508
FOXO3119525.7320.511
 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