Information
Accession GMS-65-82 (FID: 534)Browse (ALL)
Title Hi-C on sync. HeLa cells - Rep2
HiC file 4DNFIS3DIH4V (1.18 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-18 05:39:06
Last update date2025-01-18 05:39:06
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 2025-01-18 05:39:06
Reference hg38 (Human)  
Result file DomainCall.tar.gz (207.05 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 857 domains
1679 boundaries
GMS Loop 2609 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (1679)
CTCF(+) RAD21(-)  60 (3.57%)
CTCF(-) RAD21(+)  51 (3.04%)
CTCF(+) RAD21(+)  189 (11.26%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB2 40 5.025 0.533
HOXB5 59 4.616 0.519
HOXB1 67 4.564 0.519
MEIS1 138 4.451 0.510
HOXB6 67 4.169 0.527
HOXB2 43 3.654 0.511
HOXD3 43 3.596 0.511
CTCF 35 3.552 0.526
VAX2 46 3.486 0.509
GSX2 43 3.371 0.514
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (2609 x2 anchors)
CTCF(+) RAD21(-)  113 (4.33%) LA
 111 (4.25%) RA
 5 (0.19%) LA & RA
CTCF(-) RAD21(+)  65 (2.49%) LA
 72 (2.76%) RA
 3 (0.11%) LA & RA
CTCF(+) RAD21(+)  424 (16.25%) LA
 415 (15.91%) RA
 79 (3.03%) LA + RA
CTCF directionality
(2609 cases)		  54 (2.07%)Convergent ≫ ≪
 11 (0.42%)Divergent ≪ ≫
 56 (2.15%)Tandem ≫ ≫
 821 (31.47%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
RHOXF129331.8950.521
Sox543331.0680.572
FOXL129025.0360.527
MEIS130724.5330.505
FOXI127624.0650.530
FOXO427624.0650.527
FOXO627624.0650.526
FOXP327624.0650.521
NFATC217921.2050.571
Nr2e327119.8360.516
 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