Information
Accession GMS-64-54 (FID: 628)Browse (ALL)
Title Hi-C on mouse cerebellar granule neurons
HiC file 4DNFIATBSBS3 (2.67 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-10 10:47:34
Last update date2025-02-10 10:47:34
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 10:47:34
Reference mm10 (Mouse)  
Result file DomainCall.tar.gz (274.44 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 4179 domains
7716 boundaries
GMS Loop 10062 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (7716)
CTCF(+) RAD21(-)  210 (2.72%)
CTCF(-) RAD21(+)  172 (2.23%)
CTCF(+) RAD21(+)  1166 (15.11%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C 1516 22.752 0.555
ZNF518A 491 10.776 0.523
CTCF 173 10.593 0.551
RAX2 359 8.208 0.502
SHOX 330 7.375 0.500
BSX 288 6.383 0.508
FOXD1 290 6.300 0.515
FOXO3 336 6.059 0.508
NFATC2 284 5.895 0.535
HOXA4 213 5.746 0.505
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (10062 x2 anchors)
CTCF(+) RAD21(-)  361 (3.59%) LA
 336 (3.34%) RA
 18 (0.18%) LA & RA
CTCF(-) RAD21(+)  199 (1.98%) LA
 208 (2.07%) RA
 2 (0.02%) LA & RA
CTCF(+) RAD21(+)  2535 (25.19%) LA
 2427 (24.12%) RA
 773 (7.68%) LA + RA
CTCF directionality
(10068 cases)		  594 (5.9%)Convergent ≫ ≪
 66 (0.66%)Divergent ≪ ≫
 350 (3.48%)Tandem ≫ ≫
 3651 (36.26%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB286662.9060.588
CTCF80955.4330.598
NFATC2126048.1160.572
ZNF518A164842.0510.532
Sox599638.3840.562
LMX1A109832.9170.513
ISX124531.3160.497
Shox2124531.3160.513
UNCX123431.0890.510
RAX2123227.4220.509
 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