Information
Accession GMS-64-39 (FID: 606)Browse (ALL)
Title Hi-C on HFF cells - protocol variations
HiC file 4DNFIBKZK63V (2.57 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-06 10:51:14
Last update date2025-02-06 10:51:14
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 10:51:14
Reference hg38 (Human)  
Result file DomainCall.tar.gz (254.93 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 2957 domains
5656 boundaries
GMS Loop 6945 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (5656)
CTCF(+) RAD21(-)  201 (3.55%)
CTCF(-) RAD21(+)  191 (3.38%)
CTCF(+) RAD21(+)  762 (13.47%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 165 17.562 0.542
ZBTB2 156 15.411 0.542
Sox5 286 6.324 0.538
LHX1 116 5.035 0.513
RHOXF1 152 4.608 0.512
MIXL1 108 4.515 0.498
Smad4 155 4.291 0.495
HOXD8 120 4.159 0.511
HOXD4 155 4.129 0.513
HOXB5 156 4.085 0.509
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (6945 x2 anchors)
CTCF(+) RAD21(-)  212 (3.05%) LA
 263 (3.79%) RA
 11 (0.16%) LA & RA
CTCF(-) RAD21(+)  220 (3.17%) LA
 226 (3.25%) RA
 12 (0.17%) LA & RA
CTCF(+) RAD21(+)  1130 (16.27%) LA
 1161 (16.72%) RA
 225 (3.24%) LA + RA
CTCF directionality
(6945 cases)		  185 (2.66%)Convergent ≫ ≪
 21 (0.3%)Divergent ≪ ≫
 123 (1.77%)Tandem ≫ ≫
 2108 (30.35%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5110242.3290.570
CTCF49739.7820.553
ZNF518A97333.1460.515
ZBTB244431.4790.547
FOXL171928.5200.519
FOXI168628.1780.527
FOXO468628.1780.524
FOXO668628.1780.525
FOXP368628.1780.520
MEIS175527.8750.499
 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