Information
Accession GMS-64-42 (FID: 611)Browse (ALL)
Title Hi-C on HFF cells - protocol variations
HiC file 4DNFIL5K3MA1 (2.72 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-06 10:51:28
Last update date2025-02-06 10:51:28
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 10:53:46
Reference hg38 (Human)  
Result file DomainCall.tar.gz (231.64 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 2303 domains
4452 boundaries
GMS Loop 4243 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (4452)
CTCF(+) RAD21(-)  115 (2.58%)
CTCF(-) RAD21(+)  141 (3.17%)
CTCF(+) RAD21(+)  551 (12.38%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 108 9.845 0.545
VAX2 119 9.428 0.514
RHOXF1 129 8.289 0.505
ZBTB2 101 8.251 0.539
HOXB2 104 7.626 0.509
HOXD3 104 7.626 0.515
GSX2 105 7.565 0.514
HOXB5 143 7.460 0.514
ZNF354C 345 7.178 0.471
VAX1 142 6.876 0.516
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (4243 x2 anchors)
CTCF(+) RAD21(-)  170 (4.01%) LA
 172 (4.05%) RA
 15 (0.35%) LA & RA
CTCF(-) RAD21(+)  111 (2.62%) LA
 109 (2.57%) RA
 2 (0.05%) LA & RA
CTCF(+) RAD21(+)  633 (14.92%) LA
 673 (15.86%) RA
 136 (3.21%) LA + RA
CTCF directionality
(4243 cases)		  101 (2.38%)Convergent ≫ ≪
 23 (0.54%)Divergent ≪ ≫
 83 (1.96%)Tandem ≫ ≫
 1234 (29.08%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C89042.9640.456
Sox566539.2760.565
ZNF518A66129.0980.537
RHOXF137927.2510.522
ISX28327.0360.511
Shox229426.3110.512
Arid3a33126.1280.579
RAX226424.0400.509
FOXL142123.8350.514
VSX140923.5090.514
 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