Information
Accession GMS-64-45 (FID: 609)Browse (ALL)
Title Hi-C on HFF cells - protocol variations
HiC file 4DNFI8649RQJ (3.43 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-06 10:52:37
Last update date2025-02-06 10:52:37
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 10:53:35
Reference hg38 (Human)  
Result file DomainCall.tar.gz (325.42 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 4106 domains
7623 boundaries
GMS Loop 17825 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (7623)
CTCF(+) RAD21(-)  182 (2.39%)
CTCF(-) RAD21(+)  258 (3.38%)
CTCF(+) RAD21(+)  855 (11.22%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 232 22.371 0.533
ZBTB2 219 19.632 0.531
ESR2 119 3.231 0.507
NRL 119 3.231 0.518
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (17825 x2 anchors)
CTCF(+) RAD21(-)  652 (3.66%) LA
 655 (3.67%) RA
 28 (0.16%) LA & RA
CTCF(-) RAD21(+)  386 (2.17%) LA
 415 (2.33%) RA
 9 (0.05%) LA & RA
CTCF(+) RAD21(+)  2227 (12.49%) LA
 2218 (12.44%) RA
 394 (2.21%) LA + RA
CTCF directionality
(17826 cases)		  351 (1.97%)Convergent ≫ ≪
 52 (0.29%)Divergent ≪ ≫
 225 (1.26%)Tandem ≫ ≫
 4498 (25.23%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF106834.2650.543
ZBTB289822.8420.539
Nr2e3145421.1070.602
FOXN311128.8560.524
Lhx89616.3200.512
BSX6465.9080.509
GATA314245.6630.510
HOXB48655.5520.511
HOXB611305.1280.516
DBP5595.1230.513
 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