Information
Accession GMS-65-29 (FID: 476)Browse (ALL)
Title Hi-C on H1 cells - protocol variations
HiC file 4DNFI8JFOAJT (1.87 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-16 18:22:23
Last update date2025-01-16 18:22:23
Contact GMSuite GENOMEMODALITY
gmsuite AT hgc.jp
The University of Tokyo
Sharingopen access
Keywords Hi-C  4DN  contact matrix 
 Domain/Loop Calling Information

URL copied to the clipboard
Submit date 2025-01-16 18:22:23
Reference hg38 (Human)  
Result file DomainCall.tar.gz (268.01 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3574 domains
6835 boundaries
GMS Loop 6798 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (6835)
CTCF(+) RAD21(-)  249 (3.64%)
CTCF(-) RAD21(+)  186 (2.72%)
CTCF(+) RAD21(+)  880 (12.87%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
CTCF 169 12.963 0.537
Sox5 389 11.761 0.545
MEIS1 554 10.828 0.505
ZBTB2 151 9.607 0.536
PRRX1 239 9.539 0.505
NKX6-1 259 8.956 0.512
PRRX2 246 8.768 0.503
LHX9 242 8.712 0.505
HOXB1 230 8.545 0.517
LBX1 212 7.934 0.504
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (6798 x2 anchors)
CTCF(+) RAD21(-)  255 (3.75%) LA
 257 (3.78%) RA
 12 (0.18%) LA & RA
CTCF(-) RAD21(+)  222 (3.27%) LA
 231 (3.4%) RA
 8 (0.12%) LA & RA
CTCF(+) RAD21(+)  1262 (18.56%) LA
 1232 (18.12%) RA
 295 (4.34%) LA + RA
CTCF directionality
(6798 cases)		  270 (3.97%)Convergent ≫ ≪
 23 (0.34%)Divergent ≪ ≫
 139 (2.04%)Tandem ≫ ≫
 2142 (31.51%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox5110747.1320.558
CTCF51243.7330.562
ZNF354C72242.8820.456
MEIS1131438.3750.513
Arid3a57235.4890.573
ZBTB244833.3420.553
FOXL173432.4720.525
FOXP370229.9940.521
FOXO469729.3840.526
FOXO669729.3840.526
 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