Information
Accession GMS-64-37 (FID: 604)Browse (ALL)
Title Hi-C on HFF cells - protocol variations
HiC file 4DNFI6CWNUFL (2.57 GB)
 hic  mCool   Cooler-Tree
Submit date2025-02-06 10:51:07
Last update date2025-02-06 10:51:07
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 10:51:07
Reference hg38 (Human)  
Result file DomainCall.tar.gz (242.66 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 3076 domains
5836 boundaries
GMS Loop 4697 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (5836)
CTCF(+) RAD21(-)  192 (3.29%)
CTCF(-) RAD21(+)  196 (3.36%)
CTCF(+) RAD21(+)  806 (13.81%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
RHOXF1 253 17.190 0.521
MEIS1 293 15.773 0.505
FOXL1 268 14.691 0.526
FOXP3 255 13.852 0.524
FOXI1 252 13.475 0.532
FOXO4 252 13.475 0.529
FOXO6 252 13.475 0.528
ZBTB2 149 12.985 0.531
TLX2 175 12.961 0.510
ZNF354C 197 12.228 0.517
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (4697 x2 anchors)
CTCF(+) RAD21(-)  171 (3.64%) LA
 165 (3.51%) RA
 9 (0.19%) LA & RA
CTCF(-) RAD21(+)  125 (2.66%) LA
 141 (3%) RA
 2 (0.04%) LA & RA
CTCF(+) RAD21(+)  697 (14.84%) LA
 697 (14.84%) RA
 135 (2.87%) LA + RA
CTCF directionality
(4697 cases)		  118 (2.51%)Convergent ≫ ≪
 22 (0.47%)Divergent ≪ ≫
 77 (1.64%)Tandem ≫ ≫
 1296 (27.59%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
Sox574538.0100.555
Nr2e346025.0690.515
RHOXF139823.2390.521
VAX137821.8550.496
FOXL146521.1870.518
ZNF354C39620.7660.486
CTCF26420.4340.539
FOXI144720.3300.522
FOXO444720.3300.516
FOXP344720.3300.515
 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