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Table 1 Summary statistics of the ngs.plot database

From: ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

Item Count Description
Annotation sources 4 Refseq, Ensembl, ENCODE, muENCODE
Species (Genome) 17(21) Human (hg18, hg19), chimpanzee (panTro4), macaque (rheMac2), mouse (mm9, mm10), rat (rn4, rn5), cow (bosTau6), horse (equCab2), chicken (galGal4), zebrafish (Zv9), drosophila (dm3), Caenorhabditis elegans (ce6, ceX), Saccharomycer cerevisiae (sacCer3), Schizosaccharomyces pombe (Asm294), Helicobacter pylori (Asm852v1), Sulfolobus acidocaldarius (sulfAcid1), Arabidopsis thaliana (TAIR10), Zea mays (AGPv2)
Biotypes 7 TSS, TES, genebody, exon, CGI, DHS, enhancer
Gene type 5 Protein coding, lincRNA, miRNA, pseudogene, misc (everything else)
Exon types 7 canonical, promoter, polyA, variant, altDonor, altAcceptor, altBoth
CGIs 10 Hg18, hg19, mm9, mm10, rn4, rn5, bosTau6, galGal4, panTro4, rheMac2
Enhancers 9 (hg19) Url: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/
Cell types: H1hesc (default), Gm12878, Hepg2, Hmec, Hsmm, Huvec, K562, Nhek, Nhlf.
15 (mm9) Url: http://chromosome.sdsc.edu/mouse/download.html. Cell types: mESC, bone marrow, cerebellum, cortex, heart, intestine, kidney, liver, lung, MEF, olfactory bulb, placenta, spleen, testes, thymus.
DHS 125 (hg19) Url: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/. Cell types: H1hesc, A549, Gm12878, Helas3, Hepg2, Hmec, Hsmm, Hsmmtube, Huvec, K562, Lncap, Mcf7, Nhek, Th1,
Region analysis 8 ProximalPromoter, Promoter1K, Promoter3K, Genebody, Genedesert, OtherIntergenic, Pericentromere, Subtelomere
  1. Total count of functional elements is 60,520,599.