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. 2003 Jan 1;31(1):82-6.
doi: 10.1093/nar/gkg121.

NetAffx: Affymetrix probesets and annotations

Guoying Liu  1 , Ann E Loraine, Ron Shigeta, Melissa Cline, Jill Cheng, Venu Valmeekam, Shaw Sun, David Kulp, Michael A Siani-Rose
Affiliations

NetAffx: Affymetrix probesets and annotations

Guoying Liu et al. Nucleic Acids Res. .

Abstract

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.

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Figures

Figure 1
Figure 1
Netaffx data flow. Protein sequences are annotated via the GRAPA battery of HMMs and PSI-BLAST models, in addition to Pfam, BLAST and BLOCKS searches. These annotations are consolidated into a unified XML format which is then indexed and loaded into SRS. These separate databanks (Domains_PFAM, Similarity_NR, Domains_BLOCKS, Families_EC, Families_GPCR, Families_SCOP) are summarized in the main Netaffx databank, the Target databank. Other annotations in the Target databank include those extracted from public databases according to the GenBank accession number of the representative sequences, as described in the text. Links exist from the Target databank to databanks of probe sequences and consensus and exemplar sequences. SRS databanks are indicated by the scroll-like icon.
Figure 2
Figure 2
The interactive probeset query map for probeset 200697_at from the human chip set HG-U133.
Figure 3
Figure 3
Prototype interactive GO sub-graph for a set of probesets. One can rapidly generate a sub-graph for the GO terms associated with a single probeset or set of probesets. Part of the Biological Process subgraph is shown for probeset 1255_g_at for the U133 human GeneChip.
See this image and copyright information in PMC

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