Information
Accession GMS-65-65 (FID: 517)Browse (ALL)
Title Hi-C on sync. HeLa cells - Rep3
HiC file 4DNFICJ6I4DO (1.70 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-17 20:55:02
Last update date2025-01-17 20:55:02
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 20:55:02
Reference hg38 (Human)  
Result file DomainCall.tar.gz (207.54 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 1155 domains
2241 boundaries
GMS Loop 2345 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (2241)
CTCF(+) RAD21(-)  68 (3.03%)
CTCF(-) RAD21(+)  79 (3.53%)
CTCF(+) RAD21(+)  250 (11.16%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 51 5.440 0.527
TFDP1 43 3.392 0.525
HOXB1 74 3.316 0.503
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (2345 x2 anchors)
CTCF(+) RAD21(-)  87 (3.71%) LA
 74 (3.16%) RA
 3 (0.13%) LA & RA
CTCF(-) RAD21(+)  73 (3.11%) LA
 75 (3.2%) RA
 4 (0.17%) LA & RA
CTCF(+) RAD21(+)  338 (14.41%) LA
 392 (16.72%) RA
 62 (2.64%) LA + RA
CTCF directionality
(2345 cases)		  47 (2%)Convergent ≫ ≪
 8 (0.34%)Divergent ≪ ≫
 49 (2.09%)Tandem ≫ ≫
 683 (29.13%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox539330.1870.572
NFATC217624.8010.573
FOXL125124.6240.531
FOXI123923.1330.535
FOXO423923.1330.535
FOXO623923.1330.534
FOXP323923.1330.531
MEIS129122.1790.528
CTCF14016.7140.543
HOXB121316.7120.489
 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