This table lists the Data sources used for NetAffx Annotation Release 26, including the version number, if there is one, and the date of the release. Data sources that cover multiple species are listed first, followed by species-specific sources.
| Data source | Mol Type | Release Date | Version | Species | Description | Notes |
|---|---|---|---|---|---|---|
| GenBank | mRNA, peptide | 15-Apr-08 | 165 | All | full and partial mRNA records, CDS translations, and mRNA/peptide derived from organellar DNA. NR clustered (*) | |
| RefSeq | mRNA, peptide | 04-May-08 | 29 | All | mRNA records, CDS translations and mRNA/peptide derived from organellar DNA. NR clustered (*) | |
| UniProt | protein | 29-Apr-08 | 13.3 | All | Protein sequence data from both Swiss-Prot 55.3 and TrEMBL 38.3 | |
| Entrez Gene | mRNA | 11-May-08 | All | Gene information database derived from RefSeq, model organism databases, and other NCBI databases | Release date is the date downloaded | |
| dbSNP | DNA | 23-Oct-07 | 128 | Homo sapiens | SNP annotations | |
| HapMap | DNA | 31-Jan-08 | 23 | Homo sapiens | SNP genotypes | |
| DGV | DNA | 26-Jun-08 | 5 | Homo sapiens | CNV annotations | Database of Genomic Variants |
| Ensembl | mRNA, peptide | Mar-08 | 49 | Anopheles gambiae | cDNA, ncRNA, and peptide sequence including non-hypothetical, ab initio and EST-based transcripts | For D. melanogaster and S. cerevisiae, we use predicted transcripts from Ensembl and other annotated transcripts from Flybase and SGD, respectively |
| Bos taurus | ||||||
| Caenorhabditis elegans | ||||||
| Canis familiaris | ||||||
| Danio rerio | ||||||
| Drosophila melanogaster | ||||||
| Gallus gallus | ||||||
| Homo sapiens | ||||||
| Mus musculus | ||||||
| Rattus norvegicus | ||||||
| Saccharomyces cerevisiae | ||||||
| Xenopus tropicalis | ||||||
| DNA | Oct-07 | 47 (AgamP3) | Anopheles gambiae | Nuclear genome assembly | Excluded unassembled contigs. | |
| UniGene | mRNA | 09-Jan-08 | 39 | Anopheles gambiae | EST-based non-redundant gene-oriented clusters | |
| 31-Mar-08 | 66 | Arabidopsis thaliana | ||||
| 11-Apr-08 | 92 | Bos taurus | ||||
| 04-Apr-08 | 38 | Caenorhabditis elegans | ||||
| 06-Mar-08 | 22 | Canis familiaris | ||||
| 03-Jan-08 | 7 | Citrus sinensis | ||||
| 11-Apr-08 | 111 | Danio rerio | ||||
| 20-Mar-08 | 58 | Drosophila melanogaster | ||||
| 11-Apr-08 | 40 | Gallus gallus | ||||
| 30-Jan-08 | 32 | Glycine max | ||||
| 11-Apr-08 | 212 | Homo sapiens | ||||
| 30-Jan-08 | 52 | Hordeum vulgare | ||||
| 23-Feb-07 | 27 | Lycopersicon esculentum | ||||
| 31-Jan-08 | 12 | Macaca mulatta | ||||
| 03-Jan-08 | 30 | Medicago truncatula | ||||
| 11-Apr-08 | 171 | Mus musculus | ||||
| 11-Apr-08 | 74 | Oryza sativa | ||||
| 27-May-05 | 1 | Populus balsamifera | ||||
| 03-Jun-07 | 14 | Populus tremula x Populus tremuloides | ||||
| 07-Dec-07 | 8 | Populus trichocarpa | ||||
| 11-Apr-08 | 173 | Rattus norvegicus | ||||
| 26-Dec-07 | 13 | Saccharum officinarum | ||||
| 15-Jan-08 | 31 | Solanum tuberosum | ||||
| 15-Ap-08 | 34 | Sus scrofa | ||||
| 11-Apr-08 | 52 | Triticum aestivum | ||||
| 05-Dec-07 | 7 | Vitis vinifera | ||||
| 03-Feb-08 | 82 | Xenopus laevis | ||||
| 11-Apr-08 | 43 | Xenopus tropicalis | ||||
| 04-Apr-08 | 69 | Zea mays | ||||
| UCSC | DNA | Oct-07 | bosTau4 | Bos taurus | Nuclear and mitochondrial genome assemblies | |
| Jan-07 | ce4 | Caenorhabditis elegans | ||||
| May-05 | canFam2 | Canis familiaris | ||||
| Jul-07 | danRer5 | Danio rerio | ||||
| Mar-06 | hg18 | Homo sapiens | ||||
| Jul-07 | mm9 | Mus musculus | ||||
| May-06 | galGal3 | Gallus gallus | ||||
| Jan-06 | rheMac2 | Macaca mulatta | ||||
| Nov-04 | rn4 | Rattus norvegicus | ||||
| Oct-03 | sacCer1 | Saccharomyces cerevisiae | ||||
| RefSeq (bacterial & plant) | DNA, RNA, peptide | Jun-06 | Escherichia coli | Strains: MG1655, EDL933, CFT073, EcoRIMD | CDS and peptides extracted from the RefSeq genome assembly record. | May-06 | Staphyloccus aureus | Strains: N315, MU50, COL | May-06 | Bacillus subtilis |
| Mitochondrial DNA, RNA, peptide | Oct-05 | Arabidopsis thaliana | Organellar genome assembly | Gene, CDS, and peptide sequences were extracted from the RefSeq genome assembly record. | ||
| Chloroplast DNA, RNA, peptide | Oct-05 | Arabidopsis thaliana | ||||
| TIGR | DNA | 13-May-04 | Arabidopsis thaliana | Nuclear genome assembly | ||
| mRNA | 6-Oct-05 | Medicago truncatula | Predicted CDS sequences from IMGAG | |||
| DNA, mitochondrial, chloroplast | 24-Jan-07 | 5 | Oryza sativa | Rice pseudomolecules - nuclear and organellar genome assemblies | ||
| mRNA, peptide | 24-Jan-07 | 5 | Oryza sativa | Rice pseudomolecules - transcripts | ||
| DNA, mRNA | 1-Aug-04 | pfa1 | Plasmodium falciparum | Nuclear genome assembly and cDNA sequences | ||
| mRNA | 05-Jun-06 | 2 | Triticum aestivum | TIGR Plant Transcript Assemblies | ||
| miRBase | miRNA | Apr-08 | 11.0 | Homo sapiens | Precursor miRNA stem-loop sequences | Used only for annotating exon arrays. |
| Mus musculus | ||||||
| Rattus norvegicus | ||||||
| RAP | mRNA, peptide | 15-May-07 | 2 | Oryza sativa | Rice Annotation Project annotations | |
| BGI_RIS | mRNA, peptide | 1-Aug-04 | Oryza sativa | Fgene-based predictions (Syngenta) | ||
| BDGP | DNA | 29-Mar-06 | 5 | Drosophila melanogaster | Nuclear genome assembly | Same assembly used by UCSC dm3. Equivalent to FlyBase 5.3 |
| FlyBase | Mitochondrial DNA, RNA, peptide | 08-Dec-06 | 5.1 | Drosophila melanogaster | Mitochondrial genome assembly | |
| all RNA, peptide | Genome sequence annotations | |||||
| JGI | DNA | Jun-04 | 1.0 | Populus trichocarpa | Nuclear genome assembly, 7.5x coverage | |
| mRNA | 13-Sep-06 | 1.1 | Populus trichocarpa | Transcripts from predicted gene models | ||
| Pasteur Institute | mRNA, peptide | 09-Jul-04 | SLR 16.1 | Bacillus subtilis | ||
| PseudoCAP | mRNA, peptide | 12-Jul-06 | Pseudomonas aeruginosa | Pseudomonas community annotation project | Release date is the date downloaded | |
| Sanger | DNA | 4-Jul-05 | Schizosaccharomyces pombe | Nuclear genome assembly | ||
| mRNA, peptide | 17-May-06 | All ORF CDS | ||||
| SGD | mRNA, peptide | 12-May-06 | Saccharomyces cerevisiae | All ORF CDS |
