Information
Accession GMS-64-62 (FID: 644)Browse (ALL)
Title Hi-C on mouse cerebellar granule neurons
HiC file 4DNFIAXX5DW8 (2.88 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 (264.74 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3961 domains
7347 boundaries
GMS Loop 8648 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (7347)
CTCF(+) RAD21(-)  158 (2.15%)
CTCF(-) RAD21(+)  195 (2.65%)
CTCF(+) RAD21(+)  1106 (15.05%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 161 9.720 0.548
ZBTB2 156 8.888 0.548
ZNF518A 859 8.533 0.525
RAX2 350 7.927 0.505
HOXD4 263 7.849 0.505
SHOX 324 7.569 0.504
FOXN3 298 7.023 0.543
NFATC2 293 6.974 0.541
FOXO3 325 6.663 0.508
BSX 280 6.654 0.505
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (8648 x2 anchors)
CTCF(+) RAD21(-)  262 (3.03%) LA
 264 (3.05%) RA
 8 (0.09%) LA & RA
CTCF(-) RAD21(+)  184 (2.13%) LA
 183 (2.12%) RA
 1 (0.01%) LA & RA
CTCF(+) RAD21(+)  2061 (23.83%) LA
 2021 (23.37%) RA
 608 (7.03%) LA + RA
CTCF directionality
(8648 cases)		  457 (5.28%)Convergent ≫ ≪
 54 (0.62%)Divergent ≪ ≫
 258 (2.98%)Tandem ≫ ≫
 3070 (35.5%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C421895.1220.575
CTCF73158.5230.595
Arid3a143547.9300.617
ZBTB259839.6320.582
ZNF518A142937.8950.535
NFATC2103733.7070.561
Sox585031.9070.571
LMX1A91627.1650.508
GATA3109326.5800.501
FOXO398924.3860.510
 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