Information
Accession GMS-64-60 (FID: 640)Browse (ALL)
Title Hi-C on mouse cerebellar granule neurons
HiC file 4DNFILCDVPW5 (4.23 GB)
 hic mCool Cooler-Tree
Submit date2025-02-10 10:52:07
Last update date2025-02-10 10:52:07
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 2025-02-10 10:52:07
Reference mm10 (Mouse)  
Result file DomainCall.tar.gz (290.94 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 5456 domains
9793 boundaries
GMS Loop 11248 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (9793)
CTCF(+) RAD21(-)  210 (2.14%)
CTCF(-) RAD21(+)  298 (3.04%)
CTCF(+) RAD21(+)  1630 (16.64%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue
ROC
AUC
CTCF 275 20.746 0.557
ZBTB2 254 17.151 0.557
Arid3a 573 9.302 0.583
FOXD1 427 8.722 0.517
HOXC4 341 8.714 0.515
ZNF518A 1176 8.540 0.521
GATA3 514 8.024 0.495
ZNF354C 532 7.081 0.492
NFATC2 392 5.941 0.537
FOXL1 236 5.660 0.528
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (11248 x2 anchors)
CTCF(+) RAD21(-)  372 (3.31%) LA
 349 (3.1%) RA
 11 (0.1%) LA & RA
CTCF(-) RAD21(+)  259 (2.3%) LA
 262 (2.33%) RA
 9 (0.08%) LA & RA
CTCF(+) RAD21(+)  2858 (25.41%) LA
 2876 (25.57%) RA
 945 (8.4%) LA + RA
CTCF directionality
(11253 cases)
 741 (6.58%)Convergent ≫ ≪
 67 (0.6%)Divergent ≪ ≫
 392 (3.48%)Tandem ≫ ≫
 4065 (36.12%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue
ROC
AUC
CTCF97265.0490.599
ZBTB296063.5890.588
ZNF354C169848.1270.583
NFATC2129333.8020.564
GATA3140128.4540.501
HOXC4109626.1950.518
FOXD1113526.1020.522
Sox5105225.6850.560
Nr2e388725.1820.507
UNCX129325.0470.505
 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