Information
Accession GMS-64-44 (FID: 613)Browse (ALL)
Title Hi-C on HFF cells - protocol variations
HiC file 4DNFIA6NSSBJ (2.36 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-06 10:52:13
Last update date2025-02-06 10:52:13
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 2025-02-06 10:54:14
Reference hg38 (Human)  
Result file DomainCall.tar.gz (283.01 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3769 domains
7172 boundaries
GMS Loop 10049 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (7172)
CTCF(+) RAD21(-)  261 (3.64%)
CTCF(-) RAD21(+)  198 (2.76%)
CTCF(+) RAD21(+)  1040 (14.5%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 245 27.896 0.551
ZBTB2 241 26.949 0.543
ZNF354C 270 10.050 0.485
VAX1 233 9.839 0.508
Nr2e3 262 9.612 0.509
VAX2 183 9.300 0.509
NFATC2 174 8.377 0.538
HOXB2 167 8.374 0.503
HOXD3 167 8.374 0.507
RHOXF1 248 8.042 0.508
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (10049 x2 anchors)
CTCF(+) RAD21(-)  405 (4.03%) LA
 385 (3.83%) RA
 19 (0.19%) LA & RA
CTCF(-) RAD21(+)  296 (2.95%) LA
 336 (3.34%) RA
 10 (0.1%) LA & RA
CTCF(+) RAD21(+)  1814 (18.05%) LA
 1871 (18.62%) RA
 444 (4.42%) LA + RA
CTCF directionality
(10052 cases)		  373 (3.71%)Convergent ≫ ≪
 39 (0.39%)Divergent ≪ ≫
 214 (2.13%)Tandem ≫ ≫
 3229 (32.12%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF78352.2060.567
ZBTB269140.7710.559
MEIS1192630.2880.508
RHOXF184829.0370.513
ZNF354C98027.1520.530
FOXL199626.6040.525
FOXP395226.4410.525
FOXI194826.3390.531
FOXO494826.3390.529
FOXO694826.3390.529
 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