Information
Accession GMS-65-40 (FID: 487)Browse (ALL)
Title Hi-C on H1 cells
HiC file 4DNFISLZ9FR1 (4.85 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-17 13:00:51
Last update date2025-01-17 13:00:51
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 03:01:24
Reference hg38 (Human)  
Result file DomainCall.tar.gz (313.93 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 6443 domains
11553 boundaries
GMS Loop 9789 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (11553)
CTCF(+) RAD21(-)  390 (3.38%)
CTCF(-) RAD21(+)  337 (2.92%)
CTCF(+) RAD21(+)  1654 (14.32%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 357 27.449 0.545
ZBTB2 300 18.339 0.546
Sox5 674 14.955 0.545
VAX1 382 13.194 0.514
Nr2e3 414 12.760 0.515
MEIS1 506 12.421 0.512
NFATC2 287 10.666 0.541
FOXL1 417 10.426 0.520
NKX6-1 445 10.274 0.515
FOXI1 394 10.075 0.526
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (9789 x2 anchors)
CTCF(+) RAD21(-)  438 (4.47%) LA
 420 (4.29%) RA
 23 (0.23%) LA & RA
CTCF(-) RAD21(+)  328 (3.35%) LA
 340 (3.47%) RA
 16 (0.16%) LA & RA
CTCF(+) RAD21(+)  2363 (24.14%) LA
 2387 (24.38%) RA
 732 (7.48%) LA + RA
CTCF directionality
(9794 cases)		  670 (6.84%)Convergent ≫ ≪
 38 (0.39%)Divergent ≪ ≫
 290 (2.96%)Tandem ≫ ≫
 3622 (36.98%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF1254122.5500.599
Sox5175574.0330.566
ZBTB286865.9610.585
FOXL1116850.8420.538
MEIS1121747.4570.530
FOXI1111147.3230.540
FOXO4111147.3230.538
FOXO6111147.3230.537
FOXP3111147.3230.532
RHOXF198845.9950.519
 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