Gene sets

Annotation Summary

In general annotations may be associated directly with an NCBI GeneID or they may be associated with a gene product that has an assigned Uniprot accession (UniprotKB-AC) ID. All UniprotKB-AC accessions are mapped to UniprotKb-entries. To clarify the following tables.

  • taxon - matches with the taxon summary table on the top of the page
  • genes (annots) - The number of unique GeneIDs from NCBI that are associated with a given taxon
  • uniprot (annots) - The identifiers from uniprot (non-unique) that are associated with a given taxon
  • coding-genes - GeneIDs that have at least one associated uniprot identifier
  • combined - uniprot and gene annotations with redundant annotations removed
  • coverage - combined divided by genes

The combined number of annotations may be less than the total observed annotations because multiple uniprot ids may map to a single gene id.

Taxon Scientific Name Common Name
10090 Mus musculus house mouse
9606 Homo sapiens human
7227 Drosophila melanogaster fruit fly
7955 Danio rerio leopard danio

Including IEA evidence

Taxon genes (annots) uniprot (annots) coding-genes combined coverage
10090 69347 (18938) 16671 (15735) 15619 19006 27.4071
9606 47736 (18114) 140289 (100435) 18921 18244 38.2185
7227 23387 (11563) 40464 (26100) 13543 11870 50.7547
7955 36579 (14990) 2926 (2697) 2669 15069 41.1958

Excluding IEA evidence

Taxon genes (annots) uniprot (annots) coding-genes combined coverage
10090 69347 (15763) 16671 (11428) 15619 15842 22.8445
9606 47736 (14077) 140289 (17803) 18921 14263 29.8789
7227 23387 (10338) 40464 (12648) 13543 10500 44.8967
7955 36579 (3962) 2926 (1261) 2669 4006 10.9516

Other organisms

ncbi_id name total_genes total_annotations
352472 Dictyostelium discoideum AX4 13893 46815
243164 Dehalococcoides ethenogenes 195 1643 3903
214684 Cryptococcus neoformans 6618 12688
211586 Shewanella oneidensis 4591 10351
227321 Aspergillus nidulans FGSC A4 9596 31811
3702 Arabidopsis thaliana 33584 150462
7955 Danio rerio 36644 91414
9031 Gallus gallus 25998 15334
205920 Ehrlichia chaffeensis 1159 2810
7227 Drosophila melanogaster 23387 80109
176299 Agrobacterium fabrum 5465 142
246194 Carboxydothermus hydrogenoformans 2708 6282
195099 Campylobacter jejuni RM1221 1941 4557
9913 Bos taurus 43990 7634
36329 Plasmodium falciparum 3D7 5510 3448
4536 Oryza nivara 165 97
511145 Escherichia coli 4498 5292
265669 Listeria monocytogenes 2935 6977
40149 Oryza meridionalis 124 4
227377 Coxiella burnetii 2096 4449
9606 Homo sapiens,human 46263 204932
243233 Methylococcus capsulatus 3053 7166
243231 Geobacter sulfurreducens PCA 3714 7689
39946 Oryza sativa Indica Group 161 160
39947 Oryza sativa Japonica Group 30535 4740
559292 Saccharomyces cerevisiae S288c 6350 75240
284812 Schizosaccharomyces pombe 6954 35088
246200 Ruegeria pomeroyi 4349 10631
10116 Rattus norvegicus 44939 243527
10090 Mus musculus 57997 267454
212042 Anaplasma phagocytophilum str. HZ 1412 3438
4529 Oryza rufipogon 343 2
222891 Neorickettsia sennetsu 974 2392
234826 Anaplasma marginale 1005 196
999953 Trypanosoma brucei brucei 10193 1820
198094 Bacillus anthracis str. Ames,None, 5450 12398
6239 Caenorhabditis elegans,nematode, 45727 65615
223283 Pseudomonas syringae pv. 5843 9962

Gene sets used in this study