Information
Accession GMS-64-46 (FID: 612)Browse (ALL)
Title Hi-C on HFF cells - protocol variations
HiC file 4DNFIZ4F74QR (3.35 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-06 10:52:50
Last update date2025-02-06 10:52:50
Contact Sung-Joon PARK
park AT hgc.jp
The University of Tokyo
Sharingopen access
Keywords Hi-C  4DN  contact matrix 
 Domain/Loop Calling Information

URL copied to the clipboard
Submit date 2025-02-06 10:54:00
Reference hg38 (Human)  
Result file DomainCall.tar.gz (314.20 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 5416 domains
9934 boundaries
GMS Loop 11936 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (9934)
CTCF(+) RAD21(-)  377 (3.8%)
CTCF(-) RAD21(+)  276 (2.78%)
CTCF(+) RAD21(+)  1447 (14.57%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C 2498 58.878 0.548
MEIS1 538 29.706 0.518
Sox5 696 27.069 0.557
RHOXF1 426 21.899 0.514
ZBTB2 270 19.320 0.538
FOXL1 447 18.674 0.528
FOXP3 427 18.046 0.529
FOXI1 425 17.965 0.532
FOXO4 425 17.965 0.533
FOXO6 425 17.965 0.532
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (11936 x2 anchors)
CTCF(+) RAD21(-)  579 (4.85%) LA
 573 (4.8%) RA
 36 (0.3%) LA & RA
CTCF(-) RAD21(+)  286 (2.4%) LA
 344 (2.88%) RA
 12 (0.1%) LA & RA
CTCF(+) RAD21(+)  2465 (20.65%) LA
 2565 (21.49%) RA
 707 (5.92%) LA + RA
CTCF directionality
(11944 cases)		  659 (5.52%)Convergent ≫ ≪
 40 (0.33%)Divergent ≪ ≫
 341 (2.85%)Tandem ≫ ≫
 4118 (34.48%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB2111475.6460.575
CTCF105368.4210.579
ZNF354C124648.6590.443
MEIS1148048.6340.511
RHOXF1120547.2790.519
FOXL1131340.0430.525
Nr2e3124539.6660.515
FOXI1126038.5360.534
FOXO4126038.5360.532
FOXO6126038.5360.531
 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