Information
Accession GMS-64-59 (FID: 639)Browse (ALL)
Title Hi-C on mouse cerebellar granule neurons
HiC file 4DNFIXCQHKCF (2.75 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-10 10:50:52
Last update date2025-02-10 10:50:52
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 10:50:52
Reference mm10 (Mouse)  
Result file DomainCall.tar.gz (258.63 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3817 domains
7044 boundaries
GMS Loop 8234 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (7044)
CTCF(+) RAD21(-)  154 (2.19%)
CTCF(-) RAD21(+)  146 (2.07%)
CTCF(+) RAD21(+)  1123 (15.94%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 183 14.665 0.556
ZBTB2 147 8.288 0.546
ZNF518A 836 8.223 0.512
FOXD1 280 6.924 0.514
HOXC4 249 6.206 0.512
FOXO3 306 5.578 0.508
VAX2 144 5.414 0.506
FOXN3 277 4.615 0.543
VAX1 167 4.597 0.504
Smad4 314 4.537 0.505
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (8234 x2 anchors)
CTCF(+) RAD21(-)  255 (3.1%) LA
 271 (3.29%) RA
 14 (0.17%) LA & RA
CTCF(-) RAD21(+)  190 (2.31%) LA
 188 (2.28%) RA
 3 (0.04%) LA & RA
CTCF(+) RAD21(+)  1925 (23.38%) LA
 1919 (23.31%) RA
 551 (6.69%) LA + RA
CTCF directionality
(8238 cases)		  455 (5.52%)Convergent ≫ ≪
 38 (0.46%)Divergent ≪ ≫
 231 (2.8%)Tandem ≫ ≫
 2930 (35.57%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF61745.9000.591
ZBTB261645.7550.578
ZNF354C123945.3670.578
NFATC297740.8790.560
Sox579837.2050.555
ZNF518A128731.3660.528
Shox2104629.5170.501
UNCX95427.2000.499
LMX1A89425.3670.505
LHX580623.6770.504
 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