Information
Accession GMS-64-63 (FID: 646)Browse (ALL)
Title Hi-C on mouse cerebellar granule neurons
HiC file 4DNFIM7ACSX2 (2.93 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-11 11:33:30
Last update date2025-02-11 11:33:30
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 11:33:30
Reference mm10 (Mouse)  
Result file DomainCall.tar.gz (271.29 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 4354 domains
7969 boundaries
GMS Loop 9482 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (7969)
CTCF(+) RAD21(-)  206 (2.59%)
CTCF(-) RAD21(+)  170 (2.13%)
CTCF(+) RAD21(+)  1216 (15.26%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 202 14.831 0.551
HOXC4 330 10.917 0.517
FOXO3 338 7.400 0.513
FOXN3 331 7.189 0.549
NFATC2 282 6.404 0.539
ZBTB2 150 6.397 0.546
SHOX 334 6.183 0.495
ISX 364 5.973 0.491
Shox2 364 5.973 0.498
PRRX2 310 5.829 0.487
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (9482 x2 anchors)
CTCF(+) RAD21(-)  284 (3%) LA
 282 (2.97%) RA
 14 (0.15%) LA & RA
CTCF(-) RAD21(+)  232 (2.45%) LA
 243 (2.56%) RA
 5 (0.05%) LA & RA
CTCF(+) RAD21(+)  2262 (23.86%) LA
 2185 (23.04%) RA
 671 (7.08%) LA + RA
CTCF directionality
(9486 cases)		  508 (5.36%)Convergent ≫ ≪
 42 (0.44%)Divergent ≪ ≫
 302 (3.18%)Tandem ≫ ≫
 3317 (34.97%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C447485.3700.581
ZBTB274552.2720.586
CTCF72649.7400.597
NFATC2109533.7270.562
ZNF518A146631.4790.526
Sox590830.1740.563
UNCX116228.0930.506
LMX1A102627.9710.507
Shox2113124.9570.509
RAX2103621.0740.504
 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