.. xenopus supplement 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 -------------------------------- .. toctree:: :maxdepth: 1 Links --------------- * `Statistics about the current GO annotations `_ * :doc:`Information about the database used for these data ` * `Guide to GO evidence codes `_