Information
Accession GMS-65-45 (FID: 492)Browse (ALL)
Title Hi-C on GM12878 cells - protocol variations
HiC file 4DNFI9YAVTI1 (3.28 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-17 10:05:49
Last update date2025-01-17 10:05:49
Contact GMSuite GENOMEMODALITY
gmsuite 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 2025-01-17 10:05:50
Reference hg38 (Human)  
Result file DomainCall.tar.gz (303.06 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 4534 domains
8323 boundaries
GMS Loop 10904 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (8323)
CTCF(+) RAD21(-)  342 (4.11%)
CTCF(-) RAD21(+)  243 (2.92%)
CTCF(+) RAD21(+)  1074 (12.9%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB2 262 25.059 0.537
CTCF 243 21.188 0.534
ZNF518A 539 19.071 0.525
Sox5 526 17.543 0.563
PRRX2 325 14.298 0.509
LHX9 320 13.915 0.507
HOXB1 296 12.012 0.509
RHOXF1 297 11.539 0.527
Nr2e3 314 10.862 0.510
LBX1 281 10.467 0.510
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (10904 x2 anchors)
CTCF(+) RAD21(-)  474 (4.35%) LA
 466 (4.27%) RA
 22 (0.2%) LA & RA
CTCF(-) RAD21(+)  309 (2.83%) LA
 337 (3.09%) RA
 14 (0.13%) LA & RA
CTCF(+) RAD21(+)  2660 (24.39%) LA
 2689 (24.66%) RA
 897 (8.23%) LA + RA
CTCF directionality
(10912 cases)		  830 (7.61%)Convergent ≫ ≪
 34 (0.31%)Divergent ≪ ≫
 323 (2.96%)Tandem ≫ ≫
 3931 (36.02%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF1346118.4330.599
ZBTB2117995.4300.593
Sox5159338.5230.570
RHOXF1101934.4960.528
MEIS1121231.8870.527
FOXL1108029.6130.533
FOXI1103529.4790.536
FOXO4103529.4790.534
FOXO6103529.4790.533
FOXP3103529.4790.530
 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