Information
Accession GMS-64-58 (FID: 637)Browse (ALL)
Title Hi-C on mouse cerebellar granule neurons
HiC file 4DNFIJOJW15R (3.81 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-10 10:50:10
Last update date2025-02-10 10:50:10
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 10:50:10
Reference mm10 (Mouse)  
Result file DomainCall.tar.gz (288.71 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 5147 domains
9307 boundaries
GMS Loop 10901 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (9307)
CTCF(+) RAD21(-)  245 (2.63%)
CTCF(-) RAD21(+)  182 (1.96%)
CTCF(+) RAD21(+)  1486 (15.97%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 250 18.290 0.561
Arid3a 541 16.924 0.577
ZNF354C 508 15.060 0.543
ZBTB2 224 13.899 0.560
HOXC9 213 11.327 0.510
NFATC2 373 11.264 0.537
HOXB4 346 10.820 0.513
GATA3 465 10.811 0.502
Nr2e3 280 10.646 0.507
HOXC4 360 10.480 0.517
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (10901 x2 anchors)
CTCF(+) RAD21(-)  317 (2.91%) LA
 327 (3%) RA
 15 (0.14%) LA & RA
CTCF(-) RAD21(+)  311 (2.85%) LA
 314 (2.88%) RA
 7 (0.06%) LA & RA
CTCF(+) RAD21(+)  2764 (25.36%) LA
 2794 (25.63%) RA
 884 (8.11%) LA + RA
CTCF directionality
(10904 cases)		  708 (6.49%)Convergent ≫ ≪
 53 (0.49%)Divergent ≪ ≫
 354 (3.25%)Tandem ≫ ≫
 3978 (36.48%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF97568.7380.606
ZBTB287255.9640.591
ZNF354C166052.3380.587
NFATC2126839.8900.564
Sox5103230.8460.564
Shox2134329.7340.510
FOXD1110628.2610.520
Nr2e389927.8200.508
SHOX129526.6090.507
RAX2129526.6090.508
 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