Information
Accession GMS-64-62 (FID: 645)Browse (ALL)
Title Hi-C on mouse cerebellar granule neurons
HiC file 4DNFII8ZV6J4 (2.61 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-11 11:32:21
Last update date2025-02-11 11:32:21
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 11:32:21
Reference mm10 (Mouse)  
Result file DomainCall.tar.gz (258.88 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3694 domains
6876 boundaries
GMS Loop 8410 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (6876)
CTCF(+) RAD21(-)  182 (2.65%)
CTCF(-) RAD21(+)  127 (1.85%)
CTCF(+) RAD21(+)  1047 (15.23%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
FOXD1 286 11.471 0.518
CTCF 157 10.547 0.554
ZNF518A 839 10.195 0.524
HOXC4 288 9.424 0.506
ZBTB2 142 7.947 0.549
HOXB4 260 7.798 0.502
HOXD4 260 7.798 0.502
NFATC2 261 7.603 0.545
Foxj2 354 7.121 0.509
RAX2 332 5.874 0.501
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (8410 x2 anchors)
CTCF(+) RAD21(-)  257 (3.06%) LA
 277 (3.29%) RA
 10 (0.12%) LA & RA
CTCF(-) RAD21(+)  175 (2.08%) LA
 161 (1.91%) RA
 2 (0.02%) LA & RA
CTCF(+) RAD21(+)  1859 (22.1%) LA
 1876 (22.31%) RA
 551 (6.55%) LA + RA
CTCF directionality
(8410 cases)		  433 (5.15%)Convergent ≫ ≪
 43 (0.51%)Divergent ≪ ≫
 232 (2.76%)Tandem ≫ ≫
 2853 (33.92%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C143054.8280.582
Arid3a137353.1180.596
CTCF60742.8760.589
NFATC299940.4320.561
Sox582532.5380.565
LMX1A88725.9050.511
PRRX191524.4510.498
Lhx478023.7160.501
HOXB474522.6110.505
HOXD474522.6110.505
 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