Information
Accession GMS-65-43 (FID: 490)Browse (ALL)
Title Hi-C on GM12878 cells - protocol variations
HiC file 4DNFIZGCA8AH (1.74 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-17 10:05:38
Last update date2025-01-17 10:05:38
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 2025-01-17 10:05:48
Reference hg38 (Human)  
Result file DomainCall.tar.gz (252.55 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 2150 domains
4148 boundaries
GMS Loop 6514 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (4148)
CTCF(+) RAD21(-)  163 (3.93%)
CTCF(-) RAD21(+)  107 (2.58%)
CTCF(+) RAD21(+)  515 (12.42%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5 247 8.040 0.553
CTCF 91 7.231 0.536
FOXL1 146 5.992 0.522
Nr2e3 150 5.709 0.496
ZNF780A 89 5.708 0.512
FOXI1 140 5.641 0.533
FOXO4 140 5.641 0.524
FOXO6 140 5.641 0.531
FOXP3 140 5.641 0.528
HOXB1 133 5.140 0.511
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (6514 x2 anchors)
CTCF(+) RAD21(-)  236 (3.62%) LA
 270 (4.14%) RA
 12 (0.18%) LA & RA
CTCF(-) RAD21(+)  196 (3.01%) LA
 199 (3.05%) RA
 9 (0.14%) LA & RA
CTCF(+) RAD21(+)  1272 (19.53%) LA
 1371 (21.05%) RA
 382 (5.86%) LA + RA
CTCF directionality
(6516 cases)		  321 (4.93%)Convergent ≫ ≪
 21 (0.32%)Divergent ≪ ≫
 169 (2.59%)Tandem ≫ ≫
 2131 (32.7%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF66475.1230.578
ZBTB255654.7360.573
MEIS181540.5590.515
FOXL172039.7980.528
RHOXF166937.4620.522
FOXO468336.8740.531
FOXP368336.8740.527
FOXI168336.5950.533
FOXO668336.5950.530
Arid3a56633.5940.623
 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