Information
Accession GMS-65-18 (FID: 464)Browse (ALL)
Title Liquified Chromatin Hi-C on K562 cells
HiC file 4DNFIXU2KPNQ (3.54 GB)
 hic  mCool   Cooler-Tree
Submit date2025-01-16 11:33:06
Last update date2025-01-16 11:33:06
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 2025-01-16 11:33:07
Reference hg38 (Human)  
Result file DomainCall.tar.gz (225.28 MB)  
Insulation Score (4DN) 10000bin_100000win_chrAdded.bw
5000bin_100000win_chrAdded.bw
GMS Domain 2256 domains
4222 boundaries
GMS Loop 2699 loops
 Hi-C map is too sparse

Contact Matrix
Large JuiceBox 
JuiceBox-web 
Motifs in 5Kb Boundaries (4222)
CTCF(+) RAD21(-)  116 (2.75%)
CTCF(-) RAD21(+)  168 (3.98%)
CTCF(+) RAD21(+)  540 (12.79%)
GimmeMotifs 
(Pvalue < 0.001, Top10)
JASPAR#. hits-log10
Pvalue		ROC
AUC
ZNF354C 436 28.150 0.490
Sox5 325 23.864 0.563
FOXL1 218 17.234 0.525
Nr2e3 203 15.829 0.519
FOXI1 208 15.557 0.532
FOXO4 208 15.557 0.523
FOXO6 208 15.557 0.533
FOXP3 208 15.557 0.530
MEIS1 179 12.876 0.494
RHOXF1 137 12.202 0.510
 CTCF&RAD21 in Boundaries
 Raw ROC file
 Enriched_motifs.html
 All_motifs.html
Motifs in 5Kb Loop Anchors (2699 x2 anchors)
CTCF(+) RAD21(-)  112 (4.15%) LA
 117 (4.33%) RA
 5 (0.19%) LA & RA
CTCF(-) RAD21(+)  68 (2.52%) LA
 79 (2.93%) RA
 2 (0.07%) LA & RA
CTCF(+) RAD21(+)  369 (13.67%) LA
 390 (14.45%) RA
 71 (2.63%) LA + RA
CTCF directionality
(2699 cases)		  62 (2.3%)Convergent ≫ ≪
 10 (0.37%)Divergent ≪ ≫
 51 (1.89%)Tandem ≫ ≫
 742 (27.49%)Singleton ≫
GimmeMotifs 
(Pvalue < 0.001, Top10) LA+RA
JASPAR#. hits-log10
Pvalue		ROC
AUC
RHOXF136040.3400.527
MEIS137431.4560.516
NFATC225931.3670.557
FOXL134730.6570.522
FOXO633129.1150.528
FOXI133128.9210.529
FOXO433028.8860.528
FOXP333028.3100.520
Nr2e333527.3750.512
Sox518824.3910.559
 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