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NetAffx Annotation Release 33 Notes
November, 2012

This table lists the Data sources used for NetAffx Annotation Release 33, including the date of release and version number, if available. Data sources that cover multiple species are listed first, followed by species-specific sources.

Data source Mol Type Release Date Version Species Description Notes
Entrez Gene mRNA 2012-05-07 v53 All Gene information database derived from RefSeq, model organism databases, and other NCBI databases
Ensembl mRNA, peptide 2012-07-18 UMD3.1.67 Bos taurus cDNA, ncRNA, and peptide sequence including non-hypothetical, ab initio and EST-based transcripts Emsembl organisms r67, Ensembl genomes r14
GRCh37.67 Homo sapiens
NCBIM37.67 Mus musculus
UCSC DNA 2009-08-25 bosTau6 Bos taurus Nuclear and mitochondrial genome assemblies
2009-02-00 hg19 Homo sapiens
2011-12-00 mm10 Mus musculus
dbSNP DNA 2012-06-26 137 Bos taurus SNP annotations
Homo sapiens
Mus musculus
DGV DNA 2010-03-00 9 Homo sapiens CNV annotations Database of Genomic Variants
HapMap 3 DNA 2010-05-00 Draft 1 Homo sapiens SNP genotypes
Data source Mol Type Release Date Version Species Description Notes
GenBank mRNA, peptide 2012-06-15 190 All full and partial mRNA records, CDS translations, and mRNA/peptide derived from organellar DNA. NR clustered (*)
RefSeq mRNA, peptide 2012-07-09 v54 All mRNA records, CDS translations and mRNA/peptide derived from organellar DNA. NR clustered (*)
UniProt protein 2012-07-01 2012_07 All Protein sequence data from both Swiss-Prot and TrEMBL
Entrez Gene mRNA 2012-05-07 v53 All Gene information database derived from RefSeq, model organism databases, and other NCBI databases
Ensembl mRNA, peptide 2012-07-18 AgamP3.14 Anopheles gambiae cDNA, ncRNA, and peptide sequence including non-hypothetical, ab initio and EST-based transcripts Emsembl organisms r67, Ensembl genomes r14
TAIR10.14 Arabidopsis thaliana
UMD3.1.67 Bos taurus
WBcel215.14 Caenorhabditis elegans
BROADD2.67 Canis familiaris
Zv9.67 Danio rerio
BDGP5.14 Drosophila melanogaster
WASHUC2.67 Gallus gallus
V1.0.14 Glycine max
GRCh37.67 Homo sapiens
MMUL_1.67 Macaca mulatta
NCBIM37.67 Mus musculus
ASM276v1.14 Plasmodium falciparum
JGI2.0.14 Populus trichocarpa
RGSC3.4.67 Rattus norvegicus
SacCer_Apr2011.14 Saccharomyces cerevisiae
ASM294v1.14 Schizosaccharomyces pombe
Sscrofa10.2.67 Sus scrofa
IGGP_12x.14 Vitis vinifera
JGI_4.2.67 Xenopus tropicalis
AGPv2.14 Zea mays
UniGene mRNA 2010-10-17 43 Anopheles gambiae EST-based non-redundant gene-oriented clusters
2012-06-14 74 Arabidopsis thaliana
2012-06-19 101 Bos taurus
2011-01-13 51 Caenorhabditis elegans
2010-05-03 24 Canis familiaris
2011-01-04 14 Citrus sinensis
2012-06-19 126 Danio rerio
2011-01-13 72 Drosophila melanogaster
2012-06-26 45 Gallus gallus
2012-02-26 42 Glycine max
2011-07-02 12 Gossypium hirsutum
2012-03-14 232 Homo sapiens
2011-06-17 59 Hordeum vulgare
2011-03-01 17 Macaca mulatta
2011-11-21 37 Medicago truncatula
2012-06-20 193 Mus musculus
2012-06-05 86 Oryza sativa
2011-11-10 11 Populus trichocarpa
2012-01-18 192 Rattus norvegicus
2011-04-04 15 Saccharum officinarum
2012-06-19 42 Sus scrofa
2012-01-05 60 Triticum aestivum
2012-03-25 13 Vitis vinifera
2011-03-12 91 Xenopus laevis
2010-10-06 51 Xenopus tropicalis
2011-10-22 81 Zea mays
UCSC DNA 2009-08-25 bosTau6 Bos taurus Nuclear and mitochondrial genome assemblies
2008-05-00 ce6 Caenorhabditis elegans
2005-05-00 canFam2 Canis familiaris
2010-07-01 danRer7 Danio rerio
2006-05-00 galGal3 Gallus gallus
2009-02-00 hg19 Homo sapiens
2006-01-00 rheMac2 Macaca mulatta
2007-07-00 mm9 Mus musculus mm10 used to annotate MoGene 2.0 array
2004-11-00 rn4 Rattus norvegicus
2003-10-00 sacCer1 Saccharomyces cerevisiae
2009-11-00 susScr2 Sus scrofa
BGI_RIS mRNA, peptide 2004-08-01 Oryza sativa Fgene-based predictions (Syngenta)
broad-lincrna RNA 2012-05-01 Homo sapiens Broad lincRNA catalog
broad-tucp RNA 2012-05-01 Homo sapiens Broad transcripts of uncertain coding potential (TUCP) catalog
FlyBase all RNA, peptide 2012-07-16 5.46 Drosophila melanogaster Genome sequence annotations
DNA 2012-05-11 5.45 Nuclear genome assembly
JGI DNA, mitochondrial, chloroplast, 2010-11-00 1.09 Glycine max Nuclear and organellar genome assemblies and transcripts from predicted gene models based on this genome Glycine_max_Williams_82 8x Release
DNA 2010-01-00 v2 Populus trichocarpa
mRNA, peptide 2010-01-01 2 Transcripts and proteins from predicted gene models
lncRNAdb RNA 2012-05-01 Homo sapiens Long Non-Coding RNA Database
Mus musculus
Rattus norvegicus
Medicago Consortium DNA 2010-06-08 mt3 Medicago truncatula Nuclear genome assemblies
miRBase miRNA 2011-11-01 18 All Precursor miRNA stem-loop sequences
Pasteur Institute mRNA, peptide 2004-07-09 SLR 16.1 Bacillus subtilis
PseudoCAP mRNA, peptide 2006-07-12 Pseudomonas aeruginosa Pseudomonas community annotation project Release date is the date downloaded
RAP mRNA, peptide 2007-05-15 2 Oryza sativa Rice Annotation Project annotations
RefSeq (bacterial) DNA, RNA, peptide 2006-05-00 Bacillus subtilis
2006-06-00 Escherichia coli Strains: MG1655, EDL933, CFT073, EcoRIMD CDS and peptides extracted from the RefSeq genome assembly record.
2006-05-00 Staphylococcus aureus Strains: N315, MU50, COL
RGAP DNA, mitochondrial, chloroplast, 2011-07-31 7.0 Oryza sativa Rice pseudomolecules and genome annotation
Sanger DNA 2005-07-04 Schizosaccharomyces pombe Nuclear genome assembly
TAIR DNA, mitochondrial, chloroplast 2010-11-29 TAIR10 Arabidopsis thaliana Nuclear and organellar genome assemblies
mRNA Genome transcript annotations based on the current TAIR assembly
TIGR mRNA 2005-10-06 Medicago truncatula Predicted CDS sequences from IMGAG
DNA, mRNA 2004-08-01 pfa1 Plasmodium falciparum Nuclear genome assembly and cDNA sequences
mRNA 2006-06-05 2 Triticum aestivum TIGR Plant Transcript Assemblies