Information
Accession GMS-64-58 (FID: 636)Browse (ALL)
Title Hi-C on mouse cerebellar granule neurons
HiC file 4DNFIB2UXCHA (3.45 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

URL copied to the clipboard
Submit date 2025-02-10 10:50:10
Reference mm10 (Mouse)  
Result file DomainCall.tar.gz (281.98 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 4758 domains
8681 boundaries
GMS Loop 10619 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (8681)
CTCF(+) RAD21(-)  184 (2.12%)
CTCF(-) RAD21(+)  214 (2.47%)
CTCF(+) RAD21(+)  1379 (15.89%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
HOXC4 398 14.267 0.519
CTCF 208 13.117 0.557
ZNF354C 474 10.295 0.543
RAX2 432 10.078 0.504
SHOX 392 8.869 0.504
ZNF518A 530 8.663 0.526
HOXB4 347 8.366 0.515
HOXD4 347 8.366 0.513
Shox2 410 8.329 0.505
VSX1 273 8.243 0.505
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (10619 x2 anchors)
CTCF(+) RAD21(-)  279 (2.63%) LA
 286 (2.69%) RA
 11 (0.1%) LA & RA
CTCF(-) RAD21(+)  284 (2.67%) LA
 259 (2.44%) RA
 6 (0.06%) LA & RA
CTCF(+) RAD21(+)  2572 (24.22%) LA
 2579 (24.29%) RA
 804 (7.57%) LA + RA
CTCF directionality
(10622 cases)		  625 (5.88%)Convergent ≫ ≪
 53 (0.5%)Divergent ≪ ≫
 308 (2.9%)Tandem ≫ ≫
 3750 (35.3%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C507593.3760.518
CTCF91964.3680.604
ZBTB281551.3950.592
NFATC2125338.7250.562
Sox5102336.8490.567
FOXD1109334.5990.526
HOXC4113632.2190.519
LMX1A111431.6270.516
Foxj2140230.1510.517
HOXD4102130.1410.511
 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