Information
Accession GMS-64-53 (FID: 626)Browse (ALL)
Title Hi-C on mouse cerebellar granule neurons
HiC file 4DNFI64UCV78 (2.25 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-10 10:46:58
Last update date2025-02-10 10:46:58
Contact Sung-Joon PARK
park AT hgc.jp
The University of Tokyo
Sharingopen access
Keywords Hi-C  4DN  contact matrix 
 Domain/Loop Calling Information

URL copied to the clipboard
Submit date 2025-02-10 10:46:59
Reference mm10 (Mouse)  
Result file DomainCall.tar.gz (268.18 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3662 domains
6828 boundaries
GMS Loop 9544 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (6828)
CTCF(+) RAD21(-)  145 (2.12%)
CTCF(-) RAD21(+)  162 (2.37%)
CTCF(+) RAD21(+)  1101 (16.12%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C 1341 20.508 0.543
CTCF 158 10.896 0.547
HOXC4 203 8.217 0.521
ZNF518A 414 8.004 0.517
HMGXB4 132 6.486 0.522
SHOX 283 6.094 0.495
FOXD1 273 5.918 0.517
Bhlha15 226 5.912 0.502
MEIS1 1426 5.851 0.498
Smad4 256 5.621 0.500
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (9544 x2 anchors)
CTCF(+) RAD21(-)  279 (2.92%) LA
 306 (3.21%) RA
 14 (0.15%) LA & RA
CTCF(-) RAD21(+)  233 (2.44%) LA
 228 (2.39%) RA
 4 (0.04%) LA & RA
CTCF(+) RAD21(+)  2308 (24.18%) LA
 2275 (23.84%) RA
 699 (7.32%) LA + RA
CTCF directionality
(9552 cases)		  521 (5.45%)Convergent ≫ ≪
 57 (0.6%)Divergent ≪ ≫
 310 (3.25%)Tandem ≫ ≫
 3408 (35.68%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C147656.2110.588
CTCF73149.8570.603
ZBTB267142.0940.588
NFATC2110541.0590.563
Sox591537.7740.568
FOXD1100233.1040.520
Foxj2125532.2870.518
LMX1A105730.1670.504
FOXI165328.1160.528
FOXO665328.1160.529
 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