Information
Accession GMS-64-56 (FID: 633)Browse (ALL)
Title Hi-C on mouse cerebellar granule neurons
HiC file 4DNFIKR8L3O5 (2.59 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-10 10:48:27
Last update date2025-02-10 10:48:27
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 10:48:28
Reference mm10 (Mouse)  
Result file DomainCall.tar.gz (262.49 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3817 domains
7027 boundaries
GMS Loop 8843 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (7027)
CTCF(+) RAD21(-)  141 (2.01%)
CTCF(-) RAD21(+)  185 (2.63%)
CTCF(+) RAD21(+)  1070 (15.23%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C 1383 25.546 0.493
CTCF 159 10.398 0.552
ZBTB2 160 9.845 0.546
ZNF518A 826 8.092 0.525
PDX1 403 7.355 0.507
LHX9 283 6.476 0.500
PRRX2 283 6.121 0.503
Shox2 320 5.697 0.508
PRRX1 271 5.686 0.504
NKX6-2 266 5.443 0.509
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (8843 x2 anchors)
CTCF(+) RAD21(-)  264 (2.99%) LA
 254 (2.87%) RA
 8 (0.09%) LA & RA
CTCF(-) RAD21(+)  227 (2.57%) LA
 230 (2.6%) RA
 5 (0.06%) LA & RA
CTCF(+) RAD21(+)  2158 (24.4%) LA
 2094 (23.68%) RA
 640 (7.24%) LA + RA
CTCF directionality
(8845 cases)		  498 (5.63%)Convergent ≫ ≪
 49 (0.55%)Divergent ≪ ≫
 267 (3.02%)Tandem ≫ ≫
 3146 (35.57%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF74858.9510.595
ZBTB263442.9020.583
NFATC2105441.4310.568
Sox586934.3070.564
LMX1A98430.6500.505
Lhx485626.2770.499
FOXD192626.1430.521
Nr2e373125.4080.524
HOXB479222.4000.507
FOXG157721.6050.523
 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