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NetAffx Annotation Release 30 Notes
November 2009

This table lists the Data sources used for NetAffx Annotation Release 30, 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-09 173 All full and partial mRNA records, CDS translations, and mRNA/peptide derived from organellar DNA. NR clustered (*)  
RefSeq mRNA, peptide 02-Jul-09 36 All mRNA records, CDS translations and mRNA/peptide derived from organellar DNA. NR clustered (*)  
UniProt protein 01-Sep-09 15.7 All Protein sequence data from both Swiss-Prot 57.7 and TrEMBL 40.7  
IPI protein 02-Sep-09   All Protein cross references from the International Protein Index Used for annotating Ensembl transcripts
Entrez Gene mRNA 03-Sep-09   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 Aug-09 8 Homo sapiens CNV annotations Database of Genomic Variants
Ensembl mRNA, peptide Jul-09 55 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 18-Jul-08 41 Anopheles gambiae EST-based non-redundant gene-oriented clusters  
02-Feb-09 69 Arabidopsis thaliana
10-Sep-08 93 Bos taurus
16-Nov-08 43 Caenorhabditis elegans
18-Sep-08 23 Canis familiaris
28-Dec-08 11 Citrus sinensis
23-Apr-09 116 Danio rerio
23-Apr-09 64 Drosophila melanogaster
19-Sep-08 41 Gallus gallus
23-Apr-08 37 Glycine max
16-Oct-08 10 Gossypium hirsutum
24-Apr-08 7 Gossypium raimondii
30-Mar-09 219 Homo sapiens
03-Apr-09 56 Hordeum vulgare
23-Feb-07 27 Lycopersicon esculentum
08-Sep-08 13 Macaca mulatta
21-Dec-08 35 Medicago truncatula
30-Jul-09 180 Mus musculus
14-Apr-09 79 Oryza sativa
27-May-05 1 Populus balsamifera
03-Jun-07 15 Populus tremula x Populus tremuloides
28-May-08 9 Populus trichocarpa
30-Mar-09 180 Rattus norvegicus
26-Dec-07 13 Saccharum officinarum
22-Jan-09 33 Solanum tuberosum
17-Apr-09 37 Sus scrofa
06-Feb-09 55 Triticum aestivum
11-Sep-08 9 Vitis vinifera
14-Apr-09 87 Xenopus laevis
24-Mar-09 49 Xenopus tropicalis
06-Aug-09 76 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
Feb-09 hg19 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) 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  
TAIR DNA, mitochondrial, chloroplast 19-Jun-09 TAIR9 Arabidopsis thaliana Nuclear and organellar genome assemblies  
mRNA 19-Jun-09 TAIR9 Genome transcript annotations based on the TAIR9 assembly
TIGR mRNA 6-Oct-05   Medicago truncatula Predicted CDS sequences from IMGAG  
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 Mar-09 13.0 Homo sapiens Precursor miRNA stem-loop sequences Used only for annotating exon arrays.
Mus musculus
Rattus norvegicus
RGAP DNA, mitochondrial, chloroplast, mRNA, peptide 03-Jun-09 6.1 Oryza sativa Rice pseudomolecules and genome annotation Transcripts and peptides from predicted gene models based on the pseudomolecule assemblies.
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 May-09 5.17 Drosophila melanogaster Genome sequence annotations
JGI DNA, mitochondrial, chloroplast, mRNA Dec-08 1.01 Glycine max Nuclear and organellar genome assemblies and transcripts from predicted gene models based on this genome Glycine_max_Williams_82 8x Release
DNA Jun-04 1.0 Populus trichocarpa Nuclear genome assembly, 7.5x coverage  
mRNA, peptide 13-Sep-06 1.1 Transcripts and proteins 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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