Information
Accession GMS-64-63 (FID: 647)Browse (ALL)
Title Hi-C on mouse cerebellar granule neurons
HiC file 4DNFIZJHCAA7 (2.66 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 11:33:31
Reference mm10 (Mouse)  
Result file DomainCall.tar.gz (265.27 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 4028 domains
7406 boundaries
GMS Loop 9148 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (7406)
CTCF(+) RAD21(-)  155 (2.09%)
CTCF(-) RAD21(+)  182 (2.46%)
CTCF(+) RAD21(+)  1174 (15.85%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Nr2e3 765 13.730 0.500
CTCF 167 10.559 0.556
HOXC4 221 9.491 0.517
ZBTB2 146 6.851 0.551
HOXB5 261 5.892 0.513
Bhlha15 246 5.847 0.492
HOXA1 259 5.780 0.504
ISL2 206 5.401 0.516
SHOX 309 5.359 0.499
VSX1 218 5.117 0.498
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (9148 x2 anchors)
CTCF(+) RAD21(-)  250 (2.73%) LA
 275 (3.01%) RA
 10 (0.11%) LA & RA
CTCF(-) RAD21(+)  222 (2.43%) LA
 228 (2.49%) RA
 3 (0.03%) LA & RA
CTCF(+) RAD21(+)  2133 (23.32%) LA
 2114 (23.11%) RA
 646 (7.06%) LA + RA
CTCF directionality
(9151 cases)		  482 (5.27%)Convergent ≫ ≪
 39 (0.43%)Divergent ≪ ≫
 288 (3.15%)Tandem ≫ ≫
 3160 (34.53%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF77359.3700.590
ZBTB268146.6470.577
ZNF354C139136.4180.513
NFATC2108232.1460.564
FOXD191526.6590.527
SHOX98826.3970.510
Sox590425.8900.566
LMX1A100625.5760.510
Nr2e374022.3850.507
Lhx486222.1880.501
 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