Information
Accession GMS-65-71 (FID: 523)Browse (ALL)
Title Hi-C on HeLa cells - protocol variations
HiC file 4DNFIHN2QSMX (1.32 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-17 22:14:36
Last update date2025-01-17 22:14:36
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 2025-01-17 22:14:37
Reference hg38 (Human)  
Result file DomainCall.tar.gz (268.96 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 2876 domains
5491 boundaries
GMS Loop N/A
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (5491)
CTCF(+) RAD21(-)  179 (3.26%)
CTCF(-) RAD21(+)  199 (3.62%)
CTCF(+) RAD21(+)  819 (14.92%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB2 181 22.651 0.547
CTCF 179 22.118 0.546
LHX5 251 16.180 0.515
NKX6-1 234 14.014 0.512
Sox5 336 12.194 0.552
HOXB1 201 11.967 0.514
VAX1 189 11.778 0.518
HOXB6 216 11.750 0.519
RHOXF1 200 10.693 0.510
MEIS1 264 10.422 0.517
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (8032 x2 anchors)
CTCF(+) RAD21(-)  307 (3.82%) LA
 332 (4.13%) RA
 21 (0.26%) LA & RA
CTCF(-) RAD21(+)  255 (3.17%) LA
 290 (3.61%) RA
 15 (0.19%) LA & RA
CTCF(+) RAD21(+)  1715 (21.35%) LA
 1777 (22.12%) RA
 494 (6.15%) LA + RA
CTCF directionality
(8038 cases)		  403 (5.01%)Convergent ≫ ≪
 37 (0.46%)Divergent ≪ ≫
 234 (2.91%)Tandem ≫ ≫
 2795 (34.77%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB281579.3720.577
CTCF78975.0490.580
Sox5134551.6920.568
FOXI186337.3770.533
FOXO486337.3770.530
FOXO686337.3770.530
FOXP386537.3290.526
MEIS196836.6580.502
FOXL190235.8380.520
RHOXF175534.4140.523
 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