NetAffx: Affymetrix probesets and annotations

By Guoying Liu, A. Loraine, R. Shigeta, Melissa S. Cline, Jill Cheng, V. Valmeekam, Shaw Sun, D. Kulp, Michael A. Siani-Rose. Nucleic Acids Res., 2003

530 citations recorded by the source corpus.

NetAffx (http://www.affymetrix.com) details and annotates probesets on Affymetrix GeneChip microarrays. These annotations include (i) static information specific to the probeset composition; (ii) sequence annotations extracted from public databases; and (iii) protein sequence-level annotations derived from public domain programs, as well as libraries of hidden Markov models (HMMs) developed at Affymetrix. For each probeset, NetAffx lists the probe sequences, and the consensus sequence interrogated by the probes; for the larger chip sets, interactive maps display this sequence data in genomic context. Sequence annotations include Gene Ontology (GO) terms and depiction of GO graph relationships; predicted protein domains and motifs; orthologous sequences; links to relevant pathways; and links to public databases including UniGene, LocusLink, SWISS-PROT and OMIM.

Subfields: Molecular Biology

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Citations in the corpus

PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes (2003, background): “Of these gene sets, 113 are grouped according to involvement in metabolic pathways (derived from public or local curatio”
Jetset: selecting the optimal microarray probe set to represent a gene (2011, background): “In this case, a probe set with an expression pattern of interest can be mapped to a particular gene or set of transcripts using annotations from the manufacturer or from others [1-4].”
Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. (2003, background): “Finally, if the protein Identification of Ancestral Mitochondrial Genes product was detected in exactly two tissues, then the possible con- We downloaded the consensus FASTA sequences for the genes cordance measures for the gene are 4, 2, 0, 0, 2, or 4, and represented on the Affymetrix MG-U74Av2 ol”
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data (2010, methodology): “The Affymetrix probesets data and their genomic coordinates were taken from the NetAffx release of 03/2009 (5).”
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology (2004, methodology): “When combined with statistical analysis, the GOA data set is a useful resource for building pathways and can help facilitate microarray probe design to create more focused arrays (e.g. neurofunction arrays) (22,23).”
CoPub Mapper: mining MEDLINE based on search term co-publication (2005, methodology): “A human gene thesaurus was compiled from the Affymetrix HG_U95 / HG_U133 and HUGO gene annotations (HG_U95 / HG_U133 annotation files from 2002) [34,8] (Table 1).”
Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification (2005, methodology): “The expression value for each gene was determined using the MicrroArray Suite version 5.0 (MAS 5.0) software (Hubbell et al., 2002; Liu et al., 2003) with default parameters, without using the MAS 5.0 scaling and normalizing procedures.”
GSEA-P: a desktop application for Gene Set Enrichment Analysis (2007, methodology): “Several tools such as NetAffx (Liu et al., 2003) provide the ability to map a given list of genes between platforms.”
Interpretation of Shotgun Proteomic Data (2005, unknown): “A number of tools have been described recently that can link the probes from Affymetrix arrays to the UniGene cluster identifiers (87).”