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NetAffx Annotation Release 27 Notes
Nov 2008

This table lists the Data sources used for NetAffx Annotation Release 27, 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-Aug-08 167 All full and partial mRNA records, CDS translations, and mRNA/peptide derived from organellar DNA. NR clustered (*)  
RefSeq mRNA, peptide 30-Aug-08 31 All mRNA records, CDS translations and mRNA/peptide derived from organellar DNA. NR clustered (*)  
UniProt protein 02-Sep-08 14.1 All Protein sequence data from both Swiss-Prot 56.1 and TrEMBL 39.1  
IPI protein 25-Sep-08   All Protein cross references from the International Protein Index Used for annotating Ensembl transcripts
Entrez Gene mRNA 11-Sep-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 Jul-08 50 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 15-Jun-08 40 Anopheles gambiae EST-based non-redundant gene-oriented clusters  
27-Apr-08 67 Arabidopsis thaliana
11-Apr-08 92 Bos taurus
29-Jul-08 41 Caenorhabditis elegans
06-Mar-08 22 Canis familiaris
27-Jun-08 9 Citrus sinensis
27-Jun-08 113 Danio rerio
13-Jun-08 60 Drosophila melanogaster
11-Apr-08 40 Gallus gallus
23-Jul-08 34 Glycine max
17-Aug-08 215 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
17-Aug-08 175 Mus musculus
04-May-08 75 Oryza sativa
27-May-05 1 Populus balsamifera
03-Jun-07 14 Populus tremula x Populus tremuloides
07-Dec-07 8 Populus trichocarpa
03-Jun-08 175 Rattus norvegicus
26-Dec-07 13 Saccharum officinarum
15-Jan-08 31 Solanum tuberosum
15-Apr-08 34 Sus scrofa
11-Apr-08 52 Triticum aestivum
01-May-08 8 Vitis vinifera
23-Jul-08 84 Xenopus laevis
02-Jul-08 45 Xenopus tropicalis
30-Jul-08 71 Zea mays
UCSC DNA Oct-07 bosTau4 Bos taurus Nuclear and mitochondrial genome assemblies  
May-08 ce6 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  

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