Information
Accession GMS-65-104 (FID: 556)Browse (ALL)
Title Hi-C on HeLa cells - protocol variations
HiC file 4DNFIJ7OAIFQ (1.82 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-18 15:10:12
Last update date2025-01-18 15:10:12
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 15:10:12
Reference hg38 (Human)  
Result file DomainCall.tar.gz (223.68 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 2056 domains
3948 boundaries
GMS Loop 2581 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (3948)
CTCF(+) RAD21(-)  160 (4.05%)
CTCF(-) RAD21(+)  126 (3.19%)
CTCF(+) RAD21(+)  546 (13.83%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 110 12.903 0.545
ZBTB2 107 12.083 0.548
VAX1 144 9.332 0.509
MEIS1 174 9.247 0.508
Sox5 237 8.678 0.554
FOXG1 90 6.758 0.518
Nobox 113 6.587 0.516
RHOXF1 124 6.541 0.510
Smad4 118 6.516 0.511
HOXB6 154 6.352 0.512
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (2581 x2 anchors)
CTCF(+) RAD21(-)  110 (4.26%) LA
 95 (3.68%) RA
 6 (0.23%) LA & RA
CTCF(-) RAD21(+)  85 (3.29%) LA
 94 (3.64%) RA
 4 (0.15%) LA & RA
CTCF(+) RAD21(+)  550 (21.31%) LA
 531 (20.57%) RA
 148 (5.73%) LA + RA
CTCF directionality
(2581 cases)		  128 (4.96%)Convergent ≫ ≪
 14 (0.54%)Divergent ≪ ≫
 72 (2.79%)Tandem ≫ ≫
 858 (33.24%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox561084.0440.584
MEIS139949.9420.511
FOXL137445.0000.516
FOXP336243.6660.523
FOXI136043.1190.533
FOXO436043.1190.524
FOXO636043.1190.529
ZNF354C31140.3230.448
Nr2e334540.2560.503
RHOXF153139.8020.528
 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