NetAffx: Affymetrix probesets and annotations

被引：401

作者：

Liu, GY ^{[1
]}

Loraine, AE ^{[1
]}

Shigeta, R ^{[1
]}

Cline, M ^{[1
]}

Cheng, J ^{[1
]}

Valmeekam, V ^{[1
]}

Sun, S ^{[1
]}

Kulp, D ^{[1
]}

Siani-Rose, MA ^{[1
]}

机构：

[1] Affymetrix Inc, Dept Bioinformat, Emeryville, CA 94608 USA

来源：

NUCLEIC ACIDS RESEARCH | 2003年 / 31卷 / 01期

关键词：

D O I：

10.1093/nar/gkg121

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：82 / 86

页数：5

共 16 条

[1] Iterated profile searches with PSI-BLAST - a tool for discovery in protein databases
Altschul, SF
Koonin, EV
[J]. TRENDS IN BIOCHEMICAL SCIENCES, 1998, 23 (11) : 444 - 447
[2] ALTSCHUL SF, 1990, J MOL BIOL, V215, P403, DOI 10.1006/jmbi.1990.9999
[3] Gene Ontology: tool for the unification of biology
Ashburner, M
Ball, CA
Blake, JA
Botstein, D
Butler, H
Cherry, JM
Davis, AP
Dolinski, K
Dwight, SS
Eppig, JT
Harris, MA
Hill, DP
Issel-Tarver, L
Kasarskis, A
Lewis, S
Matese, JC
Richardson, JE
Ringwald, M
Rubin, GM
Sherlock, G
[J]. NATURE GENETICS, 2000, 25 (01) : 25 - 29
[4] Bateman A, 2004, NUCLEIC ACIDS RES, V32, pD138, DOI [10.1093/nar/gkp985, 10.1093/nar/gkh121, 10.1093/nar/gkr1065]
[5] GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways
Dahlquist, KD
Salomonis, N
Vranizan, K
Lawlor, SC
Conklin, BR
[J]. NATURE GENETICS, 2002, 31 (01) : 19 - 20
[6] Evolution of bioinorganic motifs in P450-containing systems
Degtyarenko, KN
Kulikova, TA
[J]. BIOCHEMICAL SOCIETY TRANSACTIONS, 2001, 29 : 139 - 147
[7] HANKS SK, 1991, METHOD ENZYMOL, V200, P38
[8] Increased coverage of protein families with the Blocks Database servers
Henikoff, JG
Greene, EA
Pietrokovski, S
Henikoff, S
[J]. NUCLEIC ACIDS RESEARCH, 2000, 28 (01) : 228 - 230
[9] Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
Krogh, A
Larsson, B
von Heijne, G
Sonnhammer, ELL
[J]. JOURNAL OF MOLECULAR BIOLOGY, 2001, 305 (03) : 567 - 580
[10] O'Donovan Claire, 2002, Brief Bioinform, V3, P275

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