Information
Accession GMS-64-40 (FID: 607)Browse (ALL)
Title Hi-C on HFF cells - protocol variations
HiC file 4DNFIPV5KFMK (2.20 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-06 10:51:16
Last update date2025-02-06 10:51:16
Contact Sung-Joon PARK
park 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 2025-02-06 10:52:18
Reference hg38 (Human)  
Result file DomainCall.tar.gz (242.55 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 2286 domains
4405 boundaries
GMS Loop 5397 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (4405)
CTCF(+) RAD21(-)  139 (3.16%)
CTCF(-) RAD21(+)  143 (3.25%)
CTCF(+) RAD21(+)  587 (13.33%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB2 109 10.294 0.537
RHOXF1 176 9.517 0.517
CTCF 101 8.439 0.542
Smad4 132 7.326 0.503
Nr2e3 176 7.063 0.508
FOXL1 174 6.757 0.522
FOXI1 166 6.403 0.523
FOXO4 166 6.403 0.521
FOXO6 166 6.403 0.521
FOXP3 166 6.403 0.517
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (5397 x2 anchors)
CTCF(+) RAD21(-)  148 (2.74%) LA
 161 (2.98%) RA
 8 (0.15%) LA & RA
CTCF(-) RAD21(+)  164 (3.04%) LA
 210 (3.89%) RA
 11 (0.2%) LA & RA
CTCF(+) RAD21(+)  878 (16.27%) LA
 896 (16.6%) RA
 183 (3.39%) LA + RA
CTCF directionality
(5397 cases)		  159 (2.95%)Convergent ≫ ≪
 16 (0.3%)Divergent ≪ ≫
 90 (1.67%)Tandem ≫ ≫
 1553 (28.78%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C119754.1190.554
Sox591350.5960.571
CTCF37834.8820.553
MEIS165331.2360.513
RHOXF151730.8940.522
FOXL157930.3900.519
ZNF518A78229.4100.527
FOXI154527.7780.523
FOXO454527.7780.515
FOXO654527.7780.521
 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