Information
Accession GMS-64-57 (FID: 634)Browse (ALL)
Title Hi-C on mouse cerebellar granule neurons
HiC file 4DNFIOYBTKML (3.31 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-10 10:49:28
Last update date2025-02-10 10:49:28
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 10:49:28
Reference mm10 (Mouse)  
Result file DomainCall.tar.gz (258.46 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3984 domains
7336 boundaries
GMS Loop 8014 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (7336)
CTCF(+) RAD21(-)  246 (3.35%)
CTCF(-) RAD21(+)  118 (1.61%)
CTCF(+) RAD21(+)  1108 (15.1%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C 1451 19.197 0.481
ZBTB2 165 10.252 0.547
CTCF 161 9.754 0.553
NKX6-3 206 9.174 0.499
BSX 289 7.574 0.505
SHOX 330 6.937 0.504
HOXD4 261 6.121 0.510
ZNF518A 815 5.914 0.524
NFATC2 273 5.790 0.536
Smad4 262 5.583 0.504
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (8014 x2 anchors)
CTCF(+) RAD21(-)  218 (2.72%) LA
 236 (2.94%) RA
 8 (0.1%) LA & RA
CTCF(-) RAD21(+)  180 (2.25%) LA
 196 (2.45%) RA
 0 (0%) LA & RA
CTCF(+) RAD21(+)  1846 (23.03%) LA
 1766 (22.04%) RA
 497 (6.2%) LA + RA
CTCF directionality
(8017 cases)		  371 (4.63%)Convergent ≫ ≪
 37 (0.46%)Divergent ≪ ≫
 226 (2.82%)Tandem ≫ ≫
 2804 (34.98%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Arid3a131263.3400.626
NFATC291645.1370.565
Sox577640.8670.570
CTCF56440.1910.587
ZBTB251933.8280.585
LMX1A83729.9570.504
GATA3100026.7350.493
Shox296126.5270.506
UNCX87325.4260.504
Foxj2103625.3430.518
 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