Information
Accession GMS-64-53 (FID: 627)Browse (ALL)
Title Hi-C on mouse cerebellar granule neurons
HiC file 4DNFI6C7TKI7 (2.48 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-10 10:46:58
Last update date2025-02-10 10:46:58
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 10:46:59
Reference mm10 (Mouse)  
Result file DomainCall.tar.gz (272.69 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3965 domains
7330 boundaries
GMS Loop 9912 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (7330)
CTCF(+) RAD21(-)  168 (2.29%)
CTCF(-) RAD21(+)  158 (2.16%)
CTCF(+) RAD21(+)  1167 (15.92%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C 1425 21.743 0.537
Foxj2 385 11.114 0.509
FOXO3 334 9.154 0.513
CTCF 157 9.102 0.552
ZBTB2 153 8.449 0.548
FOXN3 303 8.140 0.547
FOXD1 296 7.663 0.518
HOXB1 241 6.038 0.497
NKX6-1 267 5.925 0.505
LHX5 275 5.831 0.500
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (9912 x2 anchors)
CTCF(+) RAD21(-)  235 (2.37%) LA
 281 (2.83%) RA
 8 (0.08%) LA & RA
CTCF(-) RAD21(+)  288 (2.91%) LA
 266 (2.68%) RA
 3 (0.03%) LA & RA
CTCF(+) RAD21(+)  2410 (24.31%) LA
 2380 (24.01%) RA
 738 (7.45%) LA + RA
CTCF directionality
(9919 cases)		  555 (5.6%)Convergent ≫ ≪
 57 (0.57%)Divergent ≪ ≫
 303 (3.05%)Tandem ≫ ≫
 3490 (35.18%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF86764.5500.600
ZNF354C153955.6510.579
ZBTB273345.2250.587
Sox597241.7220.567
NFATC2115240.7700.563
LMX1A109540.6680.512
MEIS188439.9870.487
FOXD1105335.7060.524
Lhx494733.6510.505
GATA3124431.7470.504
 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