Information
Accession GMS-64-60 (FID: 641)Browse (ALL)
Title Hi-C on mouse cerebellar granule neurons
HiC file 4DNFIBY3K18K (4.68 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-10 10:52:07
Last update date2025-02-10 10:52:07
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 10:52:07
Reference mm10 (Mouse)  
Result file DomainCall.tar.gz (297.44 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 5806 domains
10352 boundaries
GMS Loop 11598 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (10352)
CTCF(+) RAD21(-)  246 (2.38%)
CTCF(-) RAD21(+)  259 (2.5%)
CTCF(+) RAD21(+)  1585 (15.31%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 281 19.575 0.556
ZBTB2 248 14.335 0.556
ZNF354C 556 11.085 0.552
Smad4 492 9.697 0.508
FOXD1 437 9.368 0.523
FOXN3 452 8.864 0.552
FOXO3 455 8.790 0.516
Sox5 346 8.395 0.551
Nr2e1 221 8.062 0.509
SOX18 474 8.039 0.495
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (11598 x2 anchors)
CTCF(+) RAD21(-)  344 (2.97%) LA
 357 (3.08%) RA
 10 (0.09%) LA & RA
CTCF(-) RAD21(+)  313 (2.7%) LA
 316 (2.72%) RA
 12 (0.1%) LA & RA
CTCF(+) RAD21(+)  2976 (25.66%) LA
 2965 (25.56%) RA
 978 (8.43%) LA + RA
CTCF directionality
(11604 cases)		  745 (6.42%)Convergent ≫ ≪
 70 (0.6%)Divergent ≪ ≫
 398 (3.43%)Tandem ≫ ≫
 4228 (36.44%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C5646110.8330.582
CTCF101366.7770.615
ZBTB290854.4870.602
Arid3a188146.6810.617
Sox5109533.3340.573
NFATC2133033.0490.566
GATA3148631.6270.495
LMX1A124629.0890.510
Lhx4108626.9640.502
UNCX135026.3960.507
 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