Information
Accession GMS-64-61 (FID: 642)Browse (ALL)
Title Hi-C on mouse cerebellar granule neurons
HiC file 4DNFI3EDRB1Z (2.24 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-11 11:17:16
Last update date2025-02-11 11:17:16
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 11:17:16
Reference mm10 (Mouse)  
Result file DomainCall.tar.gz (269.78 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3549 domains
6581 boundaries
GMS Loop 10370 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (6581)
CTCF(+) RAD21(-)  160 (2.43%)
CTCF(-) RAD21(+)  121 (1.84%)
CTCF(+) RAD21(+)  1043 (15.85%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 146 9.542 0.558
HOXC4 225 8.759 0.520
ZNF518A 774 8.474 0.522
ZBTB2 130 6.666 0.548
ZNF354C 326 6.395 0.483
Shox2 319 6.327 0.502
Foxj2 329 6.226 0.501
LHX5 268 6.073 0.506
UNCX 307 5.921 0.500
NKX6-1 262 5.863 0.510
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (10370 x2 anchors)
CTCF(+) RAD21(-)  312 (3.01%) LA
 359 (3.46%) RA
 14 (0.14%) LA & RA
CTCF(-) RAD21(+)  239 (2.3%) LA
 246 (2.37%) RA
 3 (0.03%) LA & RA
CTCF(+) RAD21(+)  2521 (24.31%) LA
 2485 (23.96%) RA
 756 (7.29%) LA + RA
CTCF directionality
(10378 cases)		  585 (5.64%)Convergent ≫ ≪
 50 (0.48%)Divergent ≪ ≫
 329 (3.17%)Tandem ≫ ≫
 3765 (36.28%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF86960.3300.601
ZBTB273243.3340.589
ZNF518A163441.0500.528
ZNF354C167341.0040.582
LMX1A113434.7120.510
NFATC2116029.4380.567
Lhx499028.8160.502
LHX5102525.8960.509
Sox593025.1990.567
NKX6-198924.8330.512
 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