Information
Accession GMS-65-1 (FID: 228)Browse (ALL)
Title Intra-chromosomal Hi-C contacts (mESC Rep1)
HiC file mESC1.intra (1.69 GB)
 hic  mCool   Cooler-Tree
Submit date2022-01-31 12:21:48
Last update date2025-02-08 16:03:09
Contact GMSuite GENOMEMODALITY
gmsuite AT hgc.jp
The University of Tokyo
Sharingopen access
Keywords Chromatin PHi-C Hi-C 
 Domain/Loop Calling Information

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Submit date 2025-01-11 13:01:44
Reference mm10 (Mouse)  
Result file DomainCall.tar.gz (396.52 MB)  
Insulation Score (4DN) 10000bin_100000win.bw 5000bin_100000win.bw
GMS Domain 8164 domains
13683 boundaries
GMS Loop 32989 loops Browse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (13683)
CTCF(+) RAD21(-)  381 (2.78%)
CTCF(-) RAD21(+)  323 (2.36%)
CTCF(+) RAD21(+)  2387 (17.45%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C 3159 64.814 0.508
ZNF518A 993 25.804 0.533
CTCF 342 17.700 0.570
RAX2 726 17.128 0.505
SHOX 723 16.855 0.504
NFATC2 629 16.603 0.554
HOXC4 493 14.942 0.522
HOXB4 575 14.566 0.517
HOXD4 524 14.015 0.518
Shox2 692 13.277 0.508
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (32989 x2 anchors)
CTCF(+) RAD21(-)  688 (2.09%) LA
 736 (2.23%) RA
 17 (0.05%) LA & RA
CTCF(-) RAD21(+)  785 (2.38%) LA
 801 (2.43%) RA
 32 (0.1%) LA & RA
CTCF(+) RAD21(+)  5050 (15.31%) LA
 5169 (15.67%) RA
 1261 (3.82%) LA + RA
CTCF directionality
(33005 cases)		  848 (2.57%)Convergent ≫ ≪
 164 (0.5%)Divergent ≪ ≫
 581 (1.76%)Tandem ≫ ≫
 8489 (25.72%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Nr2e3258831.3310.587
ZNF354C406925.9440.548
CTCF164424.1090.540
Sox5257921.0550.542
Smad4317920.3510.506
NFATC2310518.4970.531
ZNF518A384016.0120.509
RAX2318315.6900.499
Shox2333515.6520.498
FOXG1172315.2430.517
 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 --threads 4 -k KR -m 2000

%>java -Xmx32g -jar juicer_tools.jar hiccups --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 --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