Information
Accession GMS-64-29 (FID: 595)Browse (ALL)
Title Hi-C on HCT116
HiC file 4DNFI5Q92UVL (3.04 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-04 14:08:03
Last update date2025-02-04 14:08:03
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 2025-02-04 14:08:03
Reference hg38 (Human)  
Result file DomainCall.tar.gz (256.46 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 4334 domains
7911 boundaries
GMS Loop 6081 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (7911)
CTCF(+) RAD21(-)  267 (3.38%)
CTCF(-) RAD21(+)  222 (2.81%)
CTCF(+) RAD21(+)  1089 (13.77%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB2 197 14.135 0.538
CTCF 193 13.413 0.540
MEIS1 344 9.785 0.516
PRRX1 273 8.237 0.511
LHX9 287 7.874 0.510
PRRX2 288 7.763 0.509
HOXB6 288 7.543 0.516
NKX6-2 275 7.429 0.513
LBX1 255 6.985 0.513
GATA3 311 6.575 0.504
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (6081 x2 anchors)
CTCF(+) RAD21(-)  251 (4.13%) LA
 261 (4.29%) RA
 14 (0.23%) LA & RA
CTCF(-) RAD21(+)  195 (3.21%) LA
 199 (3.27%) RA
 8 (0.13%) LA & RA
CTCF(+) RAD21(+)  1207 (19.85%) LA
 1229 (20.21%) RA
 311 (5.11%) LA + RA
CTCF directionality
(6081 cases)		  281 (4.62%)Convergent ≫ ≪
 19 (0.31%)Divergent ≪ ≫
 133 (2.19%)Tandem ≫ ≫
 2082 (34.24%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF56662.6190.576
ZBTB250751.2010.574
Sox594036.1010.568
MEIS1120030.2500.499
RHOXF157325.5670.513
FOXL161424.7890.529
LHX956123.8100.506
NKX6-254123.4960.513
PRRX154623.4620.509
FOXP359123.4460.528
 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