Information
Accession GMS-64-57 (FID: 635)Browse (ALL)
Title Hi-C on mouse cerebellar granule neurons
HiC file 4DNFI16SK65H (2.99 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-10 10:49:28
Last update date2025-02-10 10:49:28
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 10:49:28
Reference mm10 (Mouse)  
Result file DomainCall.tar.gz (256.97 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3712 domains
6869 boundaries
GMS Loop 7876 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (6869)
CTCF(+) RAD21(-)  169 (2.46%)
CTCF(-) RAD21(+)  130 (1.89%)
CTCF(+) RAD21(+)  1026 (14.94%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 168 12.636 0.550
ZNF518A 435 12.083 0.517
ZNF354C 393 10.174 0.550
GATA3 351 9.380 0.494
HOXC4 226 8.984 0.520
Smad4 267 8.364 0.502
Nr2e3 207 7.993 0.510
FOXD1 296 7.986 0.516
FOXO3 324 7.686 0.508
VAX1 169 7.293 0.504
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (7876 x2 anchors)
CTCF(+) RAD21(-)  172 (2.18%) LA
 177 (2.25%) RA
 5 (0.06%) LA & RA
CTCF(-) RAD21(+)  237 (3.01%) LA
 266 (3.38%) RA
 7 (0.09%) LA & RA
CTCF(+) RAD21(+)  1817 (23.07%) LA
 1747 (22.18%) RA
 496 (6.3%) LA + RA
CTCF directionality
(7879 cases)		  360 (4.57%)Convergent ≫ ≪
 36 (0.46%)Divergent ≪ ≫
 202 (2.56%)Tandem ≫ ≫
 2723 (34.56%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB262750.4780.575
CTCF53036.4750.586
Sox575432.1650.563
RAX290530.0020.502
NFATC286829.1520.560
SHOX82127.2730.504
Shox293722.5990.508
LHX576321.9440.505
LMX1A82821.6460.502
GATA394621.0520.498
 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