Information
Accession GMS-65-42 (FID: 565)Browse (ALL)
Title Hi-C on H1 cells - protocol variations
HiC file 4DNFI9NDGTUJ (6.79 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-21 18:20:08
Last update date2025-01-21 18:20:08
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 2025-01-22 10:14:55
Reference hg38 (Human)  
Result file DomainCall.tar.gz (259.10 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3081 domains
5734 boundaries
GMS Loop 6032 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (5734)
CTCF(+) RAD21(-)  256 (4.46%)
CTCF(-) RAD21(+)  142 (2.48%)
CTCF(+) RAD21(+)  1072 (18.7%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5 499 39.455 0.562
CTCF 215 30.236 0.570
MEIS1 352 28.421 0.512
LHX5 183 21.612 0.507
UNCX 187 21.104 0.507
ZBTB2 179 20.592 0.558
PRRX1 265 19.817 0.502
LHX9 272 18.806 0.499
RHOXF1 246 18.582 0.516
FOXL1 295 18.554 0.529
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (6032 x2 anchors)
CTCF(+) RAD21(-)  231 (3.83%) LA
 209 (3.46%) RA
 14 (0.23%) LA & RA
CTCF(-) RAD21(+)  190 (3.15%) LA
 234 (3.88%) RA
 13 (0.22%) LA & RA
CTCF(+) RAD21(+)  1450 (24.04%) LA
 1487 (24.65%) RA
 504 (8.36%) LA + RA
CTCF directionality
(6034 cases)		  432 (7.16%)Convergent ≫ ≪
 28 (0.46%)Divergent ≪ ≫
 185 (3.07%)Tandem ≫ ≫
 2091 (34.65%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C163794.5820.553
CTCF63276.7830.598
ZBTB262174.5090.584
FOXL188871.1050.537
FOXI184466.3320.536
FOXO484466.3320.535
FOXO684466.3320.534
FOXP384466.3320.529
MEIS189858.4670.525
Nr2e379852.4140.527
 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)
%>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