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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.