Information
Accession GMS-65-35 (FID: 482)Browse (ALL)
Title Hi-C on H1 cells - protocol variations
HiC file 4DNFIILDWK8M (2.42 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-16 22:35:38
Last update date2025-01-16 22:35:38
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 2025-01-16 22:35:39
Reference hg38 (Human)  
Result file DomainCall.tar.gz (263.52 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3269 domains
6254 boundaries
GMS Loop 6430 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (6254)
CTCF(+) RAD21(-)  232 (3.71%)
CTCF(-) RAD21(+)  173 (2.77%)
CTCF(+) RAD21(+)  908 (14.52%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 216 26.717 0.542
ZBTB2 182 18.388 0.542
RHOXF1 266 15.720 0.512
MEIS1 307 11.605 0.512
HOXB5 215 10.926 0.521
NFATC2 175 10.116 0.546
Nr2e3 259 9.922 0.509
SOX18 251 9.259 0.499
VAX1 204 9.059 0.513
Lhx4 222 8.760 0.506
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (6430 x2 anchors)
CTCF(+) RAD21(-)  244 (3.79%) LA
 268 (4.17%) RA
 12 (0.19%) LA & RA
CTCF(-) RAD21(+)  195 (3.03%) LA
 182 (2.83%) RA
 4 (0.06%) LA & RA
CTCF(+) RAD21(+)  1110 (17.26%) LA
 1155 (17.96%) RA
 269 (4.18%) LA + RA
CTCF directionality
(6431 cases)		  240 (3.73%)Convergent ≫ ≪
 21 (0.33%)Divergent ≪ ≫
 133 (2.07%)Tandem ≫ ≫
 1991 (30.96%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5114853.0790.566
FOXL176643.8080.528
MEIS182443.0500.507
ZNF354C81141.5240.492
FOXP371838.6800.529
FOXO471838.4040.534
FOXI171838.1300.535
FOXO671837.8570.534
CTCF43835.0690.557
Nr2e366331.2270.522
 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