Information
Accession GMS-65-113 (FID: 766)Browse (ALL)
Title Intra-chromosomal Hi-C contacts in mESC
HiC file Merge2.intra.MQ30.ValidPairs (1.79 GB)
 hic  mCool   Cooler-Tree
Submit date2025-04-10 09:49:35
Last update date2025-04-10 09:46:16
Contact GMSuite GENOMEMODALITY
gmsuite AT hgc.jp
The University of Tokyo
Sharingopen access
Keywords  
 Domain/Loop Calling Information

URL copied to the clipboard
Submit date 2025-04-10 16:55:32
Reference mm10 (Mouse)  
Result file DomainCall.tar.gz (297.48 MB)  
Insulation Score (4DN) 10000bin_100000win.bw 5000bin_100000win.bw
GMS Domain 8717 domains
14481 boundaries
GMS Loop 10231 loops Browse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (14481)
CTCF(+) RAD21(-)  341 (2.35%)
CTCF(-) RAD21(+)  406 (2.8%)
CTCF(+) RAD21(+)  2677 (18.49%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C 3357 61.787 0.557
ZNF518A 1077 24.914 0.543
CTCF 374 19.568 0.571
LMX1A 643 15.392 0.506
ZBTB2 340 14.829 0.569
HOXB6 568 14.293 0.517
LHX5 614 13.674 0.501
HOXB1 545 13.593 0.499
NFATC2 677 13.209 0.545
GATA3 796 13.028 0.497
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (10231 x2 anchors)
CTCF(+) RAD21(-)  345 (3.37%) LA
 326 (3.19%) RA
 12 (0.12%) LA & RA
CTCF(-) RAD21(+)  229 (2.24%) LA
 276 (2.7%) RA
 9 (0.09%) LA & RA
CTCF(+) RAD21(+)  2790 (27.27%) LA
 2783 (27.2%) RA
 1029 (10.06%) LA + RA
CTCF directionality
(10238 cases)		  852 (8.32%)Convergent ≫ ≪
 39 (0.38%)Divergent ≪ ≫
 375 (3.66%)Tandem ≫ ≫
 3726 (36.39%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF109592.4570.619
ZBTB288764.0080.612
ZNF354C145642.6210.566
NFATC2114739.1260.565
LMX1A109731.8660.505
Sox596131.8260.565
Nr2e380631.3500.511
RAX2125631.1070.503
Foxj2132829.9930.519
SHOX111626.5650.506
 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 juicer_tools.jar arrowhead --ignore-sparsity --threads 4 -k KR -m 2000

%>java -Xmx32g -jar 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 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