Information
Accession GMS-65-62 (FID: 514)Browse (ALL)
Title Hi-C on HeLa cells - protocol variations
HiC file 4DNFIE5TEYK7 (1.46 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-17 20:54:18
Last update date2025-01-17 20:54:18
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 20:54:18
Reference hg38 (Human)  
Result file DomainCall.tar.gz (252.73 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 2436 domains
4681 boundaries
GMS Loop 5871 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (4681)
CTCF(+) RAD21(-)  179 (3.82%)
CTCF(-) RAD21(+)  140 (2.99%)
CTCF(+) RAD21(+)  607 (12.97%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Nobox 160 12.550 0.504
Arid3a 159 12.333 0.575
Sox5 287 11.690 0.548
VAX1 158 11.387 0.505
Shox2 115 9.802 0.512
ISX 117 9.614 0.512
SHOX 116 9.395 0.507
LHX5 110 9.164 0.513
RAX2 112 9.137 0.509
NFATC2 122 8.757 0.549
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (5871 x2 anchors)
CTCF(+) RAD21(-)  252 (4.29%) LA
 256 (4.36%) RA
 17 (0.29%) LA & RA
CTCF(-) RAD21(+)  174 (2.96%) LA
 168 (2.86%) RA
 9 (0.15%) LA & RA
CTCF(+) RAD21(+)  1064 (18.12%) LA
 1189 (20.25%) RA
 300 (5.11%) LA + RA
CTCF directionality
(5872 cases)		  245 (4.17%)Convergent ≫ ≪
 31 (0.53%)Divergent ≪ ≫
 158 (2.69%)Tandem ≫ ≫
 1895 (32.27%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF47147.0270.564
ZNF518A93139.2480.531
FOXL168337.9970.526
MEIS175737.2490.525
FOXP364736.1360.524
ZBTB240935.5820.566
FOXI164335.2890.531
FOXO464335.2890.529
FOXO664335.2890.528
Nr2e366733.4250.515
 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