Information
Accession GMS-64-59 (FID: 638)Browse (ALL)
Title Hi-C on mouse cerebellar granule neurons
HiC file 4DNFI6SETG5U (3.03 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-10 10:50:52
Last update date2025-02-10 10:50:52
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 10:50:52
Reference mm10 (Mouse)  
Result file DomainCall.tar.gz (262.89 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 4106 domains
7574 boundaries
GMS Loop 8414 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (7574)
CTCF(+) RAD21(-)  179 (2.36%)
CTCF(-) RAD21(+)  156 (2.06%)
CTCF(+) RAD21(+)  1176 (15.53%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 190 13.464 0.554
GATA3 324 7.415 0.500
HOXC4 217 7.074 0.513
ZBTB2 140 5.897 0.548
ZNF518A 870 5.873 0.518
HOXA4 174 4.975 0.506
HMGXB4 135 4.841 0.532
VSX1 229 4.673 0.491
CTCFL 131 4.588 0.528
Arid3a 396 4.366 0.565
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (8414 x2 anchors)
CTCF(+) RAD21(-)  249 (2.96%) LA
 268 (3.19%) RA
 13 (0.15%) LA & RA
CTCF(-) RAD21(+)  213 (2.53%) LA
 205 (2.44%) RA
 7 (0.08%) LA & RA
CTCF(+) RAD21(+)  1997 (23.73%) LA
 1955 (23.24%) RA
 585 (6.95%) LA + RA
CTCF directionality
(8417 cases)		  466 (5.54%)Convergent ≫ ≪
 36 (0.43%)Divergent ≪ ≫
 242 (2.88%)Tandem ≫ ≫
 2987 (35.49%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C410599.8230.584
CTCF70557.1450.593
Arid3a135653.3450.622
ZBTB259541.1570.588
NFATC2101640.0630.567
Shox2105630.0220.504
ISX106829.6390.497
Sox581729.0390.563
LHX582627.7400.499
GATA3108727.4430.500
 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