Information
Accession GMS-64-56 (FID: 632)Browse (ALL)
Title Hi-C on mouse cerebellar granule neurons
HiC file 4DNFIRC7WQD3 (2.35 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-10 10:48:27
Last update date2025-02-10 10:48:27
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 10:48:27
Reference mm10 (Mouse)  
Result file DomainCall.tar.gz (257.46 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3506 domains
6517 boundaries
GMS Loop 8626 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (6517)
CTCF(+) RAD21(-)  158 (2.42%)
CTCF(-) RAD21(+)  135 (2.07%)
CTCF(+) RAD21(+)  997 (15.3%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF518A 411 14.932 0.523
CTCF 146 9.756 0.548
FOXD1 252 6.879 0.519
PRRX1 654 6.017 0.499
NFATC2 236 5.975 0.543
ZBTB2 123 5.882 0.545
PRRX2 652 5.879 0.497
SHOX 273 5.686 0.501
Smad4 261 5.666 0.501
ZNF454 121 5.580 0.509
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (8626 x2 anchors)
CTCF(+) RAD21(-)  237 (2.75%) LA
 236 (2.74%) RA
 7 (0.08%) LA & RA
CTCF(-) RAD21(+)  250 (2.9%) LA
 259 (3%) RA
 6 (0.07%) LA & RA
CTCF(+) RAD21(+)  2109 (24.45%) LA
 2077 (24.08%) RA
 632 (7.33%) LA + RA
CTCF directionality
(8629 cases)		  479 (5.55%)Convergent ≫ ≪
 40 (0.46%)Divergent ≪ ≫
 281 (3.26%)Tandem ≫ ≫
 3065 (35.52%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C151960.7350.529
CTCF73058.6100.593
NFATC2104347.5240.561
ZBTB260440.6270.583
ZNF518A138237.5180.518
HOXD491033.3730.512
RAX2103232.7280.506
HOXB488832.1290.514
Sox582130.6570.564
LMX1A96328.6350.505
 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