Information
Accession GMS-65-94 (FID: 546)Browse (ALL)
Title Hi-C on HeLa cells - protocol variations
HiC file 4DNFIAS8LV1C (1.40 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-18 09:08:05
Last update date2025-01-18 09:08:05
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 2025-01-18 09:08:06
Reference hg38 (Human)  
Result file DomainCall.tar.gz (279.96 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3220 domains
6138 boundaries
GMS Loop 8490 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (6138)
CTCF(+) RAD21(-)  251 (4.09%)
CTCF(-) RAD21(+)  148 (2.41%)
CTCF(+) RAD21(+)  888 (14.47%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 198 22.902 0.546
Sox5 423 20.668 0.555
MEIS1 568 20.220 0.510
Arid3a 219 18.952 0.518
ZBTB2 178 18.069 0.547
RHOXF1 262 16.883 0.517
FOXL1 277 15.903 0.517
FOXO3 294 14.691 0.510
FOXI1 257 13.497 0.522
FOXO4 257 13.497 0.520
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (8490 x2 anchors)
CTCF(+) RAD21(-)  381 (4.49%) LA
 376 (4.43%) RA
 17 (0.2%) LA & RA
CTCF(-) RAD21(+)  261 (3.07%) LA
 313 (3.69%) RA
 16 (0.19%) LA & RA
CTCF(+) RAD21(+)  1828 (21.53%) LA
 1929 (22.72%) RA
 572 (6.74%) LA + RA
CTCF directionality
(8495 cases)		  484 (5.7%)Convergent ≫ ≪
 34 (0.4%)Divergent ≪ ≫
 268 (3.15%)Tandem ≫ ≫
 2952 (34.75%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF96196.8470.587
ZBTB280271.1650.577
FOXL1107252.0960.537
MEIS1113651.2850.507
FOXP3102148.8260.524
FOXI1101848.4670.531
FOXO4101648.2280.527
FOXO6101647.9130.529
RHOXF197944.7830.523
Nr2e398437.3370.504
 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