Information
Accession GMS-65-42 (FID: 564)Browse (ALL)
Title Hi-C on H1 cells - protocol variations
HiC file 4DNFI3RIKRUJ (10.96 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-21 18:20:08
Last update date2025-01-21 18:20:08
Contact GMSuite GENOMEMODALITY
gmsuite 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 2025-01-22 09:52:07
Reference hg38 (Human)  
Result file DomainCall.tar.gz (279.07 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 4128 domains
7529 boundaries
GMS Loop 8287 loops

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (7529)
CTCF(+) RAD21(-)  271 (3.6%)
CTCF(-) RAD21(+)  190 (2.52%)
CTCF(+) RAD21(+)  1247 (16.56%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C 1355 31.156 0.547
CTCF 268 31.058 0.567
ZBTB2 234 23.302 0.555
MEIS1 440 21.903 0.514
RHOXF1 347 20.255 0.514
UNCX 218 19.100 0.501
Nr2e3 331 18.307 0.511
LHX5 216 17.707 0.508
NFATC2 234 16.830 0.555
FOXL1 330 16.589 0.521
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (8287 x2 anchors)
CTCF(+) RAD21(-)  367 (4.43%) LA
 366 (4.42%) RA
 38 (0.46%) LA & RA
CTCF(-) RAD21(+)  230 (2.78%) LA
 275 (3.32%) RA
 11 (0.13%) LA & RA
CTCF(+) RAD21(+)  2087 (25.18%) LA
 2130 (25.7%) RA
 743 (8.97%) LA + RA
CTCF directionality
(8293 cases)		  690 (8.32%)Convergent ≫ ≪
 34 (0.41%)Divergent ≪ ≫
 281 (3.39%)Tandem ≫ ≫
 2952 (35.6%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF1078120.4000.607
ZBTB288587.3310.598
Sox5157283.0480.569
ZNF354C107567.3930.559
Nr2e3103962.4930.527
FOXL1108952.2020.537
MEIS1114651.4270.523
FOXI1103348.2200.538
FOXO4103348.2200.537
FOXO6103348.2200.536
 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)
%>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