Information
Accession GMS-65-44 (FID: 491)Browse (ALL)
Title Hi-C on GM12878 cells - protocol variations
HiC file 4DNFIOCW5AEM (2.60 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-17 10:05:40
Last update date2025-01-17 10:05:40
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 10:05:41
Reference hg38 (Human)  
Result file DomainCall.tar.gz (274.36 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 4016 domains
7543 boundaries
GMS Loop 7602 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (7543)
CTCF(+) RAD21(-)  243 (3.22%)
CTCF(-) RAD21(+)  224 (2.97%)
CTCF(+) RAD21(+)  948 (12.57%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5 491 20.547 0.559
RHOXF1 258 12.583 0.533
MEIS1 580 10.967 0.507
ZBTB2 169 10.463 0.530
HOXB6 271 8.768 0.512
CTCF 158 8.650 0.539
NR2C1 143 6.386 0.510
ZNF518A 151 6.360 0.530
FOXL1 273 6.296 0.518
PRRX2 264 6.231 0.496
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (7602 x2 anchors)
CTCF(+) RAD21(-)  282 (3.71%) LA
 277 (3.64%) RA
 17 (0.22%) LA & RA
CTCF(-) RAD21(+)  217 (2.85%) LA
 220 (2.89%) RA
 8 (0.11%) LA & RA
CTCF(+) RAD21(+)  1309 (17.22%) LA
 1391 (18.3%) RA
 298 (3.92%) LA + RA
CTCF directionality
(7602 cases)		  269 (3.54%)Convergent ≫ ≪
 26 (0.34%)Divergent ≪ ≫
 155 (2.04%)Tandem ≫ ≫
 2359 (31.03%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF62653.7310.565
ZBTB252037.3290.554
Sox5108336.7580.553
FOXL173828.8410.523
FOXI170226.5460.525
FOXO470226.5460.524
FOXP370226.5460.520
FOXO670226.3050.522
NFATC244719.1530.554
Foxj252218.8570.507
 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