Information
Accession GMS-64-54 (FID: 629)Browse (ALL)
Title Hi-C on mouse cerebellar granule neurons
HiC file 4DNFIVENO4G1 (2.42 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 10:47:35
Reference mm10 (Mouse)  
Result file DomainCall.tar.gz (269.05 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3832 domains
7138 boundaries
GMS Loop 9684 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (7138)
CTCF(+) RAD21(-)  128 (1.79%)
CTCF(-) RAD21(+)  196 (2.75%)
CTCF(+) RAD21(+)  1093 (15.31%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 180 13.912 0.553
ZBTB2 152 8.841 0.543
MEIS1 1556 8.528 0.512
Shox2 312 7.544 0.499
ZNF354C 366 7.107 0.545
HOXC4 229 6.851 0.518
Bhlha15 242 6.786 0.495
PRRX1 280 6.661 0.489
HOXB4 240 6.455 0.515
UNCX 281 6.217 0.493
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (9684 x2 anchors)
CTCF(+) RAD21(-)  325 (3.36%) LA
 332 (3.43%) RA
 10 (0.1%) LA & RA
CTCF(-) RAD21(+)  205 (2.12%) LA
 223 (2.3%) RA
 3 (0.03%) LA & RA
CTCF(+) RAD21(+)  2318 (23.94%) LA
 2214 (22.86%) RA
 649 (6.7%) LA + RA
CTCF directionality
(9690 cases)		  524 (5.41%)Convergent ≫ ≪
 59 (0.61%)Divergent ≪ ≫
 275 (2.84%)Tandem ≫ ≫
 3485 (35.96%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C472398.1780.585
ZBTB287968.6070.588
CTCF85565.2740.604
ZNF518A157741.9560.533
NFATC2121940.5250.565
Sox596334.0550.568
LMX1A104125.5460.501
LHX597624.9740.500
NKX6-194423.8500.505
FOXL168422.5340.533
 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