Information
Accession GMS-64-36 (FID: 603)Browse (ALL)
Title Hi-C on HFF cells - protocol variations
HiC file 4DNFIC3HAU11 (2.41 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-06 10:50:34
Last update date2025-02-06 10:50:34
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 10:50:34
Reference hg38 (Human)  
Result file DomainCall.tar.gz (286.24 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3798 domains
7187 boundaries
GMS Loop 10534 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (7187)
CTCF(+) RAD21(-)  270 (3.76%)
CTCF(-) RAD21(+)  216 (3.01%)
CTCF(+) RAD21(+)  1070 (14.89%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZBTB2 241 26.857 0.550
CTCF 234 25.226 0.558
Sox5 442 14.469 0.553
FOXP3 280 11.921 0.521
FOXI1 280 11.780 0.526
FOXO4 280 11.780 0.525
FOXO6 280 11.780 0.524
FOXL1 288 11.540 0.518
HOXB6 299 11.468 0.514
NKX6-1 256 10.295 0.514
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (10534 x2 anchors)
CTCF(+) RAD21(-)  380 (3.61%) LA
 422 (4.01%) RA
 19 (0.18%) LA & RA
CTCF(-) RAD21(+)  339 (3.22%) LA
 336 (3.19%) RA
 18 (0.17%) LA & RA
CTCF(+) RAD21(+)  1996 (18.95%) LA
 2036 (19.33%) RA
 508 (4.82%) LA + RA
CTCF directionality
(10536 cases)		  429 (4.07%)Convergent ≫ ≪
 42 (0.4%)Divergent ≪ ≫
 249 (2.36%)Tandem ≫ ≫
 3398 (32.25%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF73742.7270.570
ZBTB270539.0130.563
Sox5159135.5030.560
FOXL1102032.3300.525
FOXI197030.0490.530
FOXO497030.0490.525
FOXO697030.0490.529
FOXP397030.0490.526
ZNF518A143429.9590.523
Nr2e394623.7370.499
 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