Information
Accession GMS-64-55 (FID: 630)Browse (ALL)
Title Hi-C on mouse cerebellar granule neurons
HiC file 4DNFIASIXTZM (2.35 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-10 10:47:54
Last update date2025-02-10 10:47:54
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 10:47:54
Reference mm10 (Mouse)  
Result file DomainCall.tar.gz (246.17 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3241 domains
6072 boundaries
GMS Loop 7118 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (6072)
CTCF(+) RAD21(-)  193 (3.18%)
CTCF(-) RAD21(+)  96 (1.58%)
CTCF(+) RAD21(+)  860 (14.16%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Smad4 274 6.998 0.500
ZNF518A 723 6.728 0.521
FOXN3 241 4.940 0.543
HOXA1 219 4.777 0.504
Bhlha15 190 4.668 0.498
FOXO3 268 4.560 0.513
HMGXB4 106 4.394 0.523
CTCFL 107 4.201 0.518
LHX5 222 4.136 0.502
LIN54 271 4.071 0.508
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (7118 x2 anchors)
CTCF(+) RAD21(-)  216 (3.03%) LA
 226 (3.18%) RA
 8 (0.11%) LA & RA
CTCF(-) RAD21(+)  185 (2.6%) LA
 168 (2.36%) RA
 4 (0.06%) LA & RA
CTCF(+) RAD21(+)  1677 (23.56%) LA
 1678 (23.57%) RA
 538 (7.56%) LA + RA
CTCF directionality
(7119 cases)		  401 (5.63%)Convergent ≫ ≪
 39 (0.55%)Divergent ≪ ≫
 249 (3.5%)Tandem ≫ ≫
 2421 (34.01%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C353495.3960.518
ZNF518A115739.7250.526
CTCF48035.5100.584
NFATC284533.7050.564
ZBTB244430.0890.578
Sox570127.6950.559
FOXO384225.4930.511
FOXD172324.0920.523
FOXN375223.2260.580
LMX1A76423.0630.509
 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