Nucleic Acids Research, 2003, Vol. 31, No. 1 82-86
© 2003 Oxford University Press
NetAffx: Affymetrix probesets and annotations
Department of Bioinformatics, Affymetrix, Inc, 6550 Vallejo Street, Suite 100, Emeryville, CA 94608, USA
*To whom correspondence should be addressed. Email: guoying_liu{at}affymetrix.com
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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J. A. Horcajadas, A. Riesewijk, J. Polman, R. van Os, A. Pellicer, S. Mosselman, and C. Simon Effect of controlled ovarian hyperstimulation in IVF on endometrial gene expression profiles Mol. Hum. Reprod., March 1, 2005; 11(3): 195 - 205. [Abstract] [Full Text] [PDF]
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I. Yanai, H. Benjamin, M. Shmoish, V. Chalifa-Caspi, M. Shklar, R. Ophir, A. Bar-Even, S. Horn-Saban, M. Safran, E. Domany, et al. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification Bioinformatics, March 1, 2005; 21(5): 650 - 659. [Abstract] [Full Text] [PDF]
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M. Eszlinger, K. Krohn, K. Berger, J. Lauter, S. Kropf, M. Beck, D. Fuhrer, and R. Paschke Gene Expression Analysis Reveals Evidence for Increased Expression of Cell Cycle-Associated Genes and Gq-Protein-Protein Kinase C Signaling in Cold Thyroid Nodules J. Clin. Endocrinol. Metab., February 1, 2005; 90(2): 1163 - 1170. [Abstract] [Full Text] [PDF]
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K. Iwamoto, M. Bundo, and T. Kato Altered expression of mitochondria-related genes in postmortem brains of patients with bipolar disorder or schizophrenia, as revealed by large-scale DNA microarray analysis Hum. Mol. Genet., January 15, 2005; 14(2): 241 - 253. [Abstract] [Full Text] [PDF]
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C. B. Bigger, B. Guerra, K. M. Brasky, G. Hubbard, M. R. Beard, B. A. Luxon, S. M. Lemon, and R. E. Lanford Intrahepatic Gene Expression during Chronic Hepatitis C Virus Infection in Chimpanzees J. Virol., December 15, 2004; 78(24): 13779 - 13792. [Abstract] [Full Text] [PDF]
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S. Martinelli, M. Urosevic, A. Daryadel, P. A. Oberholzer, C. Baumann, M. F. Fey, R. Dummer, H.-U. Simon, and S. Yousefi Induction of Genes Mediating Interferon-dependent Extracellular Trap Formation during Neutrophil Differentiation J. Biol. Chem., October 15, 2004; 279(42): 44123 - 44132. [Abstract] [Full Text] [PDF]
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S. Addya, M. A. Keller, K. Delgrosso, C. M. Ponte, R. Vadigepalli, G. E. Gonye, and S. Surrey Erythroid-induced commitment of K562 cells results in clusters of differentially expressed genes enriched for specific transcription regulatory elements Physiol Genomics, September 16, 2004; 19(1): 117 - 130. [Abstract] [Full Text] [PDF]
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B. H. Mecham, D. Z. Wetmore, Z. Szallasi, Y. Sadovsky, I. Kohane, and T. J. Mariani Increased measurement accuracy for sequence-verified microarray probes Physiol Genomics, August 11, 2004; 18(3): 308 - 315. [Abstract] [Full Text] [PDF]
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M. Urosevic, P. A. Oberholzer, T. Maier, J. Hafner, E. Laine, H. Slade, B. Benninghoff, G. Burg, and R. Dummer Imiquimod Treatment Induces Expression of Opioid Growth Factor Receptor: A Novel Tumor Antigen Induced by Interferon-{alpha}? Clin. Cancer Res., August 1, 2004; 10(15): 4959 - 4970. [Abstract] [Full Text] [PDF]
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S. Yoshida, A. J. Mears, J. S. Friedman, T. Carter, S. He, E. Oh, Y. Jing, R. Farjo, G. Fleury, C. Barlow, et al. Expression profiling of the developing and mature Nrl-/- mouse retina: identification of retinal disease candidates and transcriptional regulatory targets of Nrl Hum. Mol. Genet., July 15, 2004; 13(14): 1487 - 1503. [Abstract] [Full Text] [PDF]
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M. Masseroli, D. Martucci, and F. Pinciroli GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining Nucleic Acids Res., July 1, 2004; 32(suppl_2): W293 - W300. [Abstract] [Full Text] [PDF]
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D. Groth, H. Lehrach, and S. Hennig GOblet: a platform for Gene Ontology annotation of anonymous sequence data Nucleic Acids Res., July 1, 2004; 32(suppl_2): W313 - W317. [Abstract] [Full Text] [PDF]
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S. Volinia, R. Evangelisti, F. Francioso, D. Arcelli, M. Carella, and P. Gasparini GOAL: automated Gene Ontology analysis of expression profiles Nucleic Acids Res., July 1, 2004; 32(suppl_2): W492 - W499. [Abstract] [Full Text] [PDF]
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 H. Mayer, M. Bilban, V. Kurtev, F. Gruber, O. Wagner, B. R. Binder, and R. de Martin Deciphering Regulatory Patterns of Inflammatory Gene Expression From Interleukin-1--Stimulated Human Endothelial Cells Arterioscler Thromb Vasc Biol, July 1, 2004; 24(7): 1192 - 1198. [Abstract] [Full Text] [PDF]
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P. Kunapuli, C. S. Kasyapa, L. Hawthorn, and J. K. Cowell LGI1, a Putative Tumor Metastasis Suppressor Gene, Controls in Vitro Invasiveness and Expression of Matrix Metalloproteinases in Glioma Cells through the ERK1/2 Pathway J. Biol. Chem., May 28, 2004; 279(22): 23151 - 23157. [Abstract] [Full Text] [PDF]
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K.-K. Wong, Y. T. M. Tsang, J. Shen, R. S. Cheng, Y.-M. Chang, T.-K. Man, and C. C. Lau Allelic imbalance analysis by high-density single-nucleotide polymorphic allele (SNP) array with whole genome amplified DNA Nucleic Acids Res., May 17, 2004; 32(9): e69 - e69. [Abstract] [Full Text] [PDF]
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B. C. McKay, L. J. Stubbert, C. C. Fowler, J. M. Smith, R. A. Cardamore, and J. C. Spronck Regulation of ultraviolet light-induced gene expression by gene size PNAS, April 27, 2004; 101(17): 6582 - 6586. [Abstract] [Full Text] [PDF]
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E. S. Lein, X. Zhao, and F. H. Gage Defining a Molecular Atlas of the Hippocampus Using DNA Microarrays and High-Throughput In Situ Hybridization J. Neurosci., April 14, 2004; 24(15): 3879 - 3889. [Abstract] [Full Text] [PDF]
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A. Hansson, N. Hance, E. Dufour, A. Rantanen, K. Hultenby, D. A. Clayton, R. Wibom, and N.-G. Larsson A switch in metabolism precedes increased mitochondrial biogenesis in respiratory chain-deficient mouse hearts PNAS, March 2, 2004; 101(9): 3136 - 3141. [Abstract] [Full Text] [PDF]
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E. Camon, M. Magrane, D. Barrell, V. Lee, E. Dimmer, J. Maslen, D. Binns, N. Harte, R. Lopez, and R. Apweiler The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology Nucleic Acids Res., January 1, 2004; 32(90001): D262 - 266. [Abstract] [Full Text] [PDF]
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C. Wiederkehr, R. Basavaraj, C. Sarrauste de Menthiere, L. Hermida, R. Koch, U. Schlecht, A. Amon, S. Brachat, M. Breitenbach, P. Briza, et al. GermOnline, a cross-species community knowledgebase on germ cell differentiation Nucleic Acids Res., January 1, 2004; 32(90001): D560 - 567. [Abstract] [Full Text] [PDF]
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