Information
Accession GMS-65-46 (FID: 493)Browse (ALL)
Title Hi-C on GM12878 cells - protocol variations
HiC file 4DNFI5CGQ46V (3.01 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-17 10:05:53
Last update date2025-01-17 10:05:53
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 10:05:54
Reference hg38 (Human)  
Result file DomainCall.tar.gz (284.96 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3735 domains
6967 boundaries
GMS Loop 8410 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (6967)
CTCF(+) RAD21(-)  242 (3.47%)
CTCF(-) RAD21(+)  225 (3.23%)
CTCF(+) RAD21(+)  992 (14.24%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5 539 28.366 0.572
MEIS1 368 18.042 0.519
RHOXF1 309 17.401 0.529
CTCF 184 15.418 0.542
Nr2e3 316 15.327 0.510
ZNF354C 294 14.151 0.523
ZBTB2 173 12.810 0.539
GATA3 336 12.574 0.506
HOXB1 286 11.671 0.504
FOXL1 310 11.528 0.512
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (8410 x2 anchors)
CTCF(+) RAD21(-)  359 (4.27%) LA
 363 (4.32%) RA
 19 (0.23%) LA & RA
CTCF(-) RAD21(+)  241 (2.87%) LA
 244 (2.9%) RA
 11 (0.13%) LA & RA
CTCF(+) RAD21(+)  1810 (21.52%) LA
 1854 (22.05%) RA
 510 (6.06%) LA + RA
CTCF directionality
(8411 cases)		  465 (5.53%)Convergent ≫ ≪
 39 (0.46%)Divergent ≪ ≫
 216 (2.57%)Tandem ≫ ≫
 2948 (35.05%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF94695.6090.582
ZBTB282675.9890.575
Sox5148864.5270.575
FOXL196747.4520.529
Nr2e394344.8750.518
FOXP392644.7220.531
ZNF354C95144.2750.463
FOXO492044.0020.537
FOXI192043.6890.538
FOXO692043.6890.536
 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