Information
Accession GMS-64-41 (FID: 608)Browse (ALL)
Title Hi-C on HFF cells - protocol variations
HiC file 4DNFIYIAUEPW (1.89 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-06 10:51:23
Last update date2025-02-06 10:51:23
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 10:52:26
Reference hg38 (Human)  
Result file DomainCall.tar.gz (279.56 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3605 domains
6890 boundaries
GMS Loop 9064 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (6890)
CTCF(+) RAD21(-)  259 (3.76%)
CTCF(-) RAD21(+)  205 (2.98%)
CTCF(+) RAD21(+)  994 (14.43%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
RHOXF1 270 19.552 0.509
FOXL1 322 18.592 0.515
FOXI1 312 18.067 0.525
FOXO4 312 18.067 0.523
FOXO6 312 18.067 0.524
FOXP3 312 18.067 0.519
CTCF 190 17.013 0.543
NFATC2 222 16.831 0.554
Nr2e3 314 15.479 0.517
Foxj2 229 14.618 0.510
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (9064 x2 anchors)
CTCF(+) RAD21(-)  391 (4.31%) LA
 428 (4.72%) RA
 30 (0.33%) LA & RA
CTCF(-) RAD21(+)  230 (2.54%) LA
 227 (2.5%) RA
 5 (0.06%) LA & RA
CTCF(+) RAD21(+)  1747 (19.27%) LA
 1781 (19.65%) RA
 458 (5.05%) LA + RA
CTCF directionality
(9066 cases)		  400 (4.41%)Convergent ≫ ≪
 48 (0.53%)Divergent ≪ ≫
 225 (2.48%)Tandem ≫ ≫
 3005 (33.15%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF79062.6900.573
Sox5150048.4720.567
ZBTB264842.9450.565
Nr2e388432.1930.516
MEIS1108331.8980.508
FOXL195930.5490.530
TEAD354029.2240.506
FOXI190628.6820.533
FOXO490628.6820.532
FOXO690628.6820.532
 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