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Platform GPL1339 Query DataSets for GPL1339
Status Public on Jul 09, 2004
Title [S_aureus] Affymetrix S. aureus Genome Array
Technology type in situ oligonucleotide
Distribution commercial
Organism Staphylococcus aureus
Manufacturer Affymetrix
Manufacture protocol see manufacturer's web site

For comprehensive monitoring of the relative mRNA abundance of S. aureus sequences.

The GeneChip S. aureus Genome Array is useful for studying the expression of sequences in the following four strains of Staphylococcus aureus: N315 (National Institute of Technology and Evaluation, Japan), Mu50 (National Institute of Technology and Evaluation, Japan), NCTC 8325 (University of Oklahoma), and COL (TIGR).

The array contains probe sets to over 3,300 S. aureus open reading frames. Additionally, the array also contains probes to study both forward and reverse orientation of over 4,800 intergenic regions throughout the S. aureus genome.
 
Description Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

June 03, 2009: annotation table updated with netaffx build 28
Oct 18, 2012: annotation table updated with netaffx build 32
 
Web link http://www.affymetrix.com/support/technical/byproduct.affx?product=saureus
http://www.affymetrix.com/analysis/index.affx
Submission date Jul 09, 2004
Last update date Oct 18, 2012
Organization Affymetrix, Inc.
E-mail(s) [email protected], [email protected]
Phone 888-362-2447
URL http://www.affymetrix.com/index.affx
Street address
City Santa Clara
State/province CA
ZIP/Postal code 95051
Country USA
 
Samples (542) GSM77043, GSM77044, GSM77045, GSM77046, GSM77047, GSM77048 
Series (55)
GSE3415 Global Transcriptome Analysis of Staphylococcus aureus Response to Hydrogen Peroxide
GSE4184 Toxicogenomic Response of Staphylococcus aureus to Peracetic Acid
GSE5498 Toxicogenomic response to chlorination includes induction of major virulence genes in Staphylococcus aureus

Data table header descriptions
ID Affymetrix Probe Set ID
PT_ACC Protein accession numbers
GeneChip Array
Species Scientific Name The genus and species of the organism represented by the probe set.
Annotation Date The date that the annotations for this probe array were last updated. It will generally be earlier than the date when the annotations were posted on the Affymetrix web site.
Sequence Type Indicates whether the sequence is an Exemplar, Consensus or Control sequence. An Exemplar is a single nucleotide sequence taken directly from a public database. This sequence could be an mRNA or EST. A Consensus sequence, is a nucleotide sequence assembled by Affymetrix, based on one or more sequence taken from a public database.
Transcript ID(Array Design)
Target Description GenBank description associated with the representative public identifier. Blank for some probe sets.
Representative Public ID The accession number of a representative sequence. Note that for consensus-based probe sets, the representative sequence is only one of several sequences (sequence sub-clusters) used to build the consensus sequence and it is not directly used to derive the probe sequences. The representative sequence is chosen during array design as a sequence that is best associated with the transcribed region being interrogated by the probe set. Refer to the "Sequence Source" field to determine the database used.
UniGene ID
Gene Title
Gene Symbol
Chromosomal Location
Entrez Gene
Gene Ontology Biological Process Gene Ontology Consortium Biological Process derived from LocusLink. Each annotation consists of three parts: "Accession Number // Description // Evidence". The description corresponds directly to the GO ID. The evidence can be "direct", or "extended".
Gene Ontology Cellular Component Gene Ontology Consortium Cellular Component derived from LocusLink. Each annotation consists of three parts: "Accession Number // Description // Evidence". The description corresponds directly to the GO ID. The evidence can be "direct", or "extended".
Gene Ontology Molecular Function Gene Ontology Consortium Molecular Function derived from LocusLink. Each annotation consists of three parts: "Accession Number // Description // Evidence". The description corresponds directly to the GO ID. The evidence can be "direct", or "extended".
Annotation Description
SPOT_ID Column added by GEO staff to facilitate sequence tracking in Entrez GEO Profiles

Data table
ID PT_ACC GeneChip Array Species Scientific Name Annotation Date Sequence Type Transcript ID(Array Design) Target Description Representative Public ID UniGene ID Gene Title Gene Symbol Chromosomal Location Entrez Gene Gene Ontology Biological Process Gene Ontology Cellular Component Gene Ontology Molecular Function Annotation Description SPOT_ID
sa_c3870s3341_a_at A5JQI0 Q5HEK4 Q7A4P8 Q99SX1 S. aureus Array Staphylococcus aureus 9-Jun-11 Consensus sa_c3870s3341 ref|NP_113934.1 solute carrier family 13 (sodium-dependent dicarboxylate transpo; solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2 [Rattus norvegicus] match=10.31% identical sa_c3870s3341 --- --- --- --- --- 0006810 // transport // inferred from electronic annotation /// 0006811 // ion transport // inferred from electronic annotation /// 0006814 // sodium ion transport // inferred from electronic annotation /// 0055085 // transmembrane transport // inferred from electronic annotation 0005886 // plasma membrane // inferred from electronic annotation /// 0016020 // membrane // inferred from electronic annotation /// 0016021 // integral to membrane // inferred from electronic annotation 0005215 // transporter activity // inferred from electronic annotation /// 0015293 // symporter activity // inferred from electronic annotation This probe set was annotated using the Matching Probes based pipeline to a GenBank identifier using 1 transcripts. // false // Matching Probes // A
sa_c118s9456_at O54520 Q5HJW4 Q7A8C7 S. aureus Array Staphylococcus aureus 9-Jun-11 Consensus sa_c118s9456 ref|NP_280923.1 monoamine oxidase regulatory-like; MaoC1 [Halobacterium sp. NRC-1] match=7.37% identical sa_c118s9456 --- --- --- --- --- 0008152 // metabolic process // inferred from electronic annotation --- 0016491 // oxidoreductase activity // inferred from electronic annotation This probe set was annotated using the Matching Probes based pipeline to a GenBank identifier using 1 transcripts. // false // Matching Probes // A
sa_c469s298_a_at O86490 Q931U9 Q99V72 S. aureus Array Staphylococcus aureus 9-Jun-11 Consensus sa_c469s298 sp|Q99V72|RF3_STAAN Peptide chain release factor 3 (RF-3) [] match=97.03% identical sa_c469s298 --- --- --- --- --- 0006412 // translation // inferred from electronic annotation /// 0006415 // translational termination // inferred from electronic annotation 0005737 // cytoplasm // inferred from electronic annotation 0000166 // nucleotide binding // inferred from electronic annotation /// 0003924 // GTPase activity // inferred from electronic annotation /// 0005525 // GTP binding // inferred from electronic annotation /// 0016149 // translation release factor activity, codon specific // inferred from electronic annotation This probe set was annotated using the Matching Probes based pipeline to a GenBank identifier using 1 transcripts. // false // Matching Probes // A
sa_c10637s11092cv_s_at O86490 Q931V0 Q99V72 S. aureus Array Staphylococcus aureus 9-Jun-11 Consensus sa_c10637s11092cv ref|NP_371544.1 peptide chain release factor 3 [Staphylococcus aureus subsp. aureus Mu50] match=48.06% identical sa_c10637s11092cv --- --- --- --- --- 0006412 // translation // inferred from electronic annotation /// 0006415 // translational termination // inferred from electronic annotation 0005737 // cytoplasm // inferred from electronic annotation 0000166 // nucleotide binding // inferred from electronic annotation /// 0003924 // GTPase activity // inferred from electronic annotation /// 0005525 // GTP binding // inferred from electronic annotation /// 0016149 // translation release factor activity, codon specific // inferred from electronic annotation This probe set was annotated using the Matching Probes based pipeline to a GenBank identifier using 1 transcripts. // false // Matching Probes // A
sa_c459s9094_a_at O86491 P65479 P65480 S. aureus Array Staphylococcus aureus 9-Jun-11 Consensus sa_c459s9094 sp|Q99V74|MURE_STAAM UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase (UDP-N-acetylmuramyl-tripeptide synthetase) (Meso-diaminopimelate-adding enzyme) (UDP-MurNAc-tripeptide synthetase) [] match=97.03% identical sa_c459s9094 --- --- --- --- --- 0007047 // cellular cell wall organization // inferred from electronic annotation /// 0007049 // cell cycle // inferred from electronic annotation /// 0008360 // regulation of cell shape // inferred from electronic annotation /// 0009058 // biosynthetic process // inferred from electronic annotation /// 0009252 // peptidoglycan biosynthetic process // inferred from electronic annotation /// 0009273 // peptidoglycan-based cell wall biogenesis // inferred from electronic annotation /// 0051301 // cell division // inferred from electronic annotation 0005737 // cytoplasm // inferred from electronic annotation 0000166 // nucleotide binding // inferred from electronic annotation /// 0005524 // ATP binding // inferred from electronic annotation /// 0016874 // ligase activity // inferred from electronic annotation /// 0016881 // acid-amino acid ligase activity // inferred from electronic annotation /// 0047482 // UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase activity // inferred from electronic annotation This probe set was annotated using the Matching Probes based pipeline to a GenBank identifier using 1 transcripts. // false // Matching Probes // A
sa_c110s9447_a_at O87369 Q7A8D0 S. aureus Array Staphylococcus aureus 9-Jun-11 Consensus sa_c110s9447 gb|AAC61950.1| aminoglycoside adenyltransferase AadD [Staphylococcus aureus] match=89.35% identical sa_c110s9447 --- --- --- --- --- 0046677 // response to antibiotic // inferred from electronic annotation --- 0016740 // transferase activity // inferred from electronic annotation /// 0016779 // nucleotidyltransferase activity // inferred from electronic annotation This probe set was annotated using the Matching Probes based pipeline to a GenBank identifier using 1 transcripts. // false // Matching Probes // A
sa_c8453s7413_a_at P00644 Q5HHM4 Q7A6P2 Q99VJ0 S. aureus Array Staphylococcus aureus 9-Jun-11 Consensus sa_c8453s7413 sp|P00644|NUC_STAAU Thermonuclease precursor (TNase) (Micrococcal nuclease) (Staphylococcal nuclease) [] match=81.98% identical sa_c8453s7413 --- --- --- --- --- --- 0005576 // extracellular region // inferred from electronic annotation /// 0016020 // membrane // inferred from electronic annotation 0003676 // nucleic acid binding // inferred from electronic annotation /// 0004518 // nuclease activity // inferred from electronic annotation /// 0004519 // endonuclease activity // inferred from electronic annotation /// 0016787 // hydrolase activity // inferred from electronic annotation /// 0016788 // hydrolase activity, acting on ester bonds // inferred from electronic annotation /// 0046872 // metal ion binding // inferred from electronic annotation This probe set was annotated using the Matching Probes based pipeline to a GenBank identifier using 1 transcripts. // false // Matching Probes // A
sa_c10629s11085_at P03064 S. aureus Array Staphylococcus aureus 9-Jun-11 Consensus sa_c10629s11085 sp|P03064|REPC_STAAU REPLICATION INITIATION PROTEIN (PROTEIN A) [] match=96.03% identical sa_c10629s11085 --- --- --- --- --- --- --- --- This probe set was annotated using the Design Representative Id based pipeline to a Affymetrix Proprietary Database identifier using 1 transcripts. // false // Design Representative Id // R
sa_c1264s1041_at P0A001 P0A002 Q5HGK0 S. aureus Array Staphylococcus aureus 9-Jun-11 Consensus sa_c1264s1041 sp|P02901|ACP_ECOLI Acyl carrier protein (ACP) (Cytosolic activating factor) (CAF) (Fatty acid synthase acyl carrier protein) [] match=38.54% identical sa_c1264s1041 --- --- --- --- --- 0006633 // fatty acid biosynthetic process // inferred from electronic annotation /// 0008610 // lipid biosynthetic process // inferred from electronic annotation /// 0046677 // response to antibiotic // inferred from electronic annotation 0005737 // cytoplasm // inferred from electronic annotation 0000036 // acyl carrier activity // inferred from electronic annotation /// 0031177 // phosphopantetheine binding // inferred from electronic annotation /// 0048037 // cofactor binding // inferred from electronic annotation This probe set was annotated using the Matching Probes based pipeline to a GenBank identifier using 1 transcripts. // false // Matching Probes // A
sa_c232s9559_a_at P0A007 P0A008 S. aureus Array Staphylococcus aureus 9-Jun-11 Consensus sa_c232s9559 sp|Q9XBA9|ATKB_STAAM Potassium-transporting ATPase B chain (Potassium-translocating ATPase B chain) (ATP phosphohydrolase [potassium-transporting] B chain) (Potassium binding and translocating subunit B) [] match=85.63% identical sa_c232s9559 --- --- --- --- --- 0006754 // ATP biosynthetic process // inferred from electronic annotation /// 0006810 // transport // inferred from electronic annotation /// 0006811 // ion transport // inferred from electronic annotation /// 0006813 // potassium ion transport // inferred from electronic annotation /// 0008152 // metabolic process // inferred from electronic annotation 0005886 // plasma membrane // inferred from electronic annotation /// 0016020 // membrane // inferred from electronic annotation /// 0016021 // integral to membrane // inferred from electronic annotation 0000166 // nucleotide binding // inferred from electronic annotation /// 0000287 // magnesium ion binding // inferred from electronic annotation /// 0003824 // catalytic activity // inferred from electronic annotation /// 0005524 // ATP binding // inferred from electronic annotation /// 0008556 // potassium-transporting ATPase activity // inferred from electronic annotation /// 0015662 // ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism // inferred from electronic annotation /// 0016787 // hydrolase activity // inferred from electronic annotation /// 0016820 // hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances // inferred from electronic annotation /// 0046872 // metal ion binding // inferred from electronic annotation This probe set was annotated using the Matching Probes based pipeline to a GenBank identifier using 1 transcripts. // false // Matching Probes // A
sa_c4703s4023_a_at P0A009 P0A010 Q5HE13 S. aureus Array Staphylococcus aureus 9-Jun-11 Consensus sa_c4703s4023 sp|P11100|LACD_STAAM Tagatose 1,6-diphosphate aldolase (Tagatose-bisphosphate aldolase) (D-tagatose-1,6-bisphosphate aldolase) [] match=76.67% identical sa_c4703s4023 --- --- --- --- --- 0005988 // lactose metabolic process // inferred from electronic annotation /// 0008152 // metabolic process // inferred from electronic annotation /// 0019512 // lactose catabolic process via tagatose-6-phosphate // inferred from electronic annotation --- 0003824 // catalytic activity // inferred from electronic annotation /// 0009024 // tagatose-6-phosphate kinase activity // inferred from electronic annotation /// 0009025 // tagatose-bisphosphate aldolase activity // inferred from electronic annotation /// 0016829 // lyase activity // inferred from electronic annotation This probe set was annotated using the Matching Probes based pipeline to a GenBank identifier using 1 transcripts. // false // Matching Probes // A
sa_c4124s3479_a_at P0A012 P99104 Q5HEH1 Q7BGE7 Q8VTM6 Q8VTM7 Q8VTM8 S. aureus Array Staphylococcus aureus 9-Jun-11 Consensus sa_c4124s3479 sp|P80469|CH10_RICTY 10 kDa chaperonin (Protein Cpn10) (groES protein) (10 kDa heat shock protein) (HSP10) [] match=24.05% identical sa_c4124s3479 --- --- --- --- --- 0006457 // protein folding // inferred from electronic annotation /// 0006950 // response to stress // inferred from electronic annotation /// 0042026 // protein refolding // inferred from electronic annotation /// 0044267 // cellular protein metabolic process // inferred from electronic annotation 0005737 // cytoplasm // inferred from electronic annotation 0000166 // nucleotide binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from electronic annotation /// 0005524 // ATP binding // inferred from electronic annotation /// 0051082 // unfolded protein binding // inferred from electronic annotation This probe set was annotated using the Matching Probes based pipeline to a GenBank identifier using 1 transcripts. // false // Matching Probes // A
sa_c1082s9604cv_s_at P0A015 P99134 Q5HJQ8 S. aureus Array Staphylococcus aureus 9-Jun-11 Consensus sa_c1082s9604cv sp|P38507|SPA2_STAAU Immunoglobulin G binding protein A precursor (IGG binding protein A) [] match=86.64% identical sa_c1082s9604cv --- --- --- --- --- 0009405 // pathogenesis // inferred from electronic annotation /// 0016998 // cell wall macromolecule catabolic process // inferred from electronic annotation 0005576 // extracellular region // inferred from electronic annotation /// 0005618 // cell wall // inferred from electronic annotation /// 0009986 // cell surface // inferred from electronic annotation /// 0016020 // membrane // inferred from electronic annotation 0005515 // protein binding // inferred from electronic annotation /// 0019864 // IgG binding // inferred from electronic annotation /// 0019865 // immunoglobulin binding // inferred from electronic annotation This probe set was annotated using the Matching Probes based pipeline to a GenBank identifier using 1 transcripts. // false // Matching Probes // A
sa_c9751s8495_a_at P0A016 P99079 Q5HFZ7 S. aureus Array Staphylococcus aureus 9-Jun-11 Consensus sa_c9751s8495 sp|Q57452|DYR8_ECOLI DIHYDROFOLATE REDUCTASE TYPE VIII (DHFR TYPE IIIC) [] match=7.15% identical sa_c9751s8495 --- --- --- --- --- 0006545 // glycine biosynthetic process // inferred from electronic annotation /// 0006730 // one-carbon metabolic process // inferred from electronic annotation /// 0009165 // nucleotide biosynthetic process // inferred from electronic annotation /// 0055114 // oxidation reduction // inferred from electronic annotation --- 0004146 // dihydrofolate reductase activity // inferred from electronic annotation /// 0016491 // oxidoreductase activity // inferred from electronic annotation /// 0050661 // NADP or NADPH binding // inferred from electronic annotation This probe set was annotated using the Matching Probes based pipeline to a GenBank identifier using 1 transcripts. // false // Matching Probes // A
sa_c8607s7564_at P0A018 P0A019 Q5HHF0 S. aureus Array Staphylococcus aureus 9-Jun-11 Consensus sa_c8607s7564 sp|Q53663|DLTC_STAAM D-alanine--poly(phosphoribitol)ligase subunit 2 (D-alanyl carrier protein) (DCP) [] match=28.89% identical sa_c8607s7564 --- --- --- --- --- 0007047 // cellular cell wall organization // inferred from electronic annotation /// 0008360 // regulation of cell shape // inferred from electronic annotation /// 0019350 // teichoic acid biosynthetic process // inferred from electronic annotation --- 0000036 // acyl carrier activity // inferred from electronic annotation /// 0000166 // nucleotide binding // inferred from electronic annotation /// 0005524 // ATP binding // inferred from electronic annotation /// 0016874 // ligase activity // inferred from electronic annotation /// 0047473 // D-alanine-poly(phosphoribitol) ligase activity // inferred from electronic annotation /// 0048037 // cofactor binding // inferred from electronic annotation This probe set was annotated using the Matching Probes based pipeline to a GenBank identifier using 1 transcripts. // false // Matching Probes // A
sa_c5s6_a_at P0A022 P99103 Q5HJZ4 S. aureus Array Staphylococcus aureus 9-Jun-11 Consensus sa_c5s6 pir|S62836 DNA-directed DNA polymerase (EC 2.7.7.7) III beta chain dnaN [Mycoplasma pneumoniae (strain ATCC 29342)] match=9.96% identical sa_c5s6 --- --- --- --- --- 0006260 // DNA replication // inferred from electronic annotation 0005737 // cytoplasm // inferred from electronic annotation 0003677 // DNA binding // inferred from electronic annotation /// 0003887 // DNA-directed DNA polymerase activity // inferred from electronic annotation /// 0008408 // 3'-5' exonuclease activity // inferred from electronic annotation /// 0016740 // transferase activity // inferred from electronic annotation /// 0016779 // nucleotidyltransferase activity // inferred from electronic annotation This probe set was annotated using the Matching Probes based pipeline to a GenBank identifier using 1 transcripts. // false // Matching Probes // A
sa_c2875s2441_a_at P0A025 P0A026 Q5HFD0 S. aureus Array Staphylococcus aureus 9-Jun-11 Consensus sa_c2875s2441 ref|NP_010062.1 D-Tyr-tRNA(Tyr) deacylase; Dtd1p [Saccharomyces cerevisiae] match=26.09% identical sa_c2875s2441 --- --- --- --- --- 0019478 // D-amino acid catabolic process // inferred from electronic annotation 0005737 // cytoplasm // inferred from electronic annotation 0016787 // hydrolase activity // inferred from electronic annotation /// 0016788 // hydrolase activity, acting on ester bonds // inferred from electronic annotation This probe set was annotated using the Matching Probes based pipeline to a GenBank identifier using 1 transcripts. // false // Matching Probes // A
sa_c9999s8695_a_at P0A029 P99108 Q5HGP5 S. aureus Array Staphylococcus aureus 9-Jun-11 Consensus sa_c9999s8695 dbj|BAB99548.1| Cell division GTPase and cell division protein ftsz [Corynebacterium glutamicum ATCC 13032] match=18.39% identical sa_c9999s8695 --- --- --- --- --- 0000917 // barrier septum formation // inferred from electronic annotation /// 0007049 // cell cycle // inferred from electronic annotation /// 0051258 // protein polymerization // inferred from electronic annotation /// 0051301 // cell division // inferred from electronic annotation 0005737 // cytoplasm // inferred from electronic annotation /// 0043234 // protein complex // inferred from electronic annotation 0000166 // nucleotide binding // inferred from electronic annotation /// 0003924 // GTPase activity // inferred from electronic annotation /// 0005525 // GTP binding // inferred from electronic annotation This probe set was annotated using the Matching Probes based pipeline to a GenBank identifier using 1 transcripts. // false // Matching Probes // A
sa_c9665s8423_a_at P0A032 P0A033 Q5HFK6 S. aureus Array Staphylococcus aureus 9-Jun-11 Consensus sa_c9665s8423 sp|P54574|FUR_BACSU Ferric uptake regulation protein (Ferric uptake regulator) [] match=9.24% identical sa_c9665s8423 --- --- --- --- --- 0006350 // transcription // inferred from electronic annotation /// 0006355 // regulation of transcription, DNA-dependent // inferred from electronic annotation /// 0045449 // regulation of transcription // inferred from electronic annotation 0005737 // cytoplasm // inferred from electronic annotation 0003677 // DNA binding // inferred from electronic annotation /// 0003700 // sequence-specific DNA binding transcription factor activity // inferred from electronic annotation /// 0046872 // metal ion binding // inferred from electronic annotation This probe set was annotated using the Matching Probes based pipeline to a GenBank identifier using 1 transcripts. // false // Matching Probes // A
sa_c8986s7896_a_at P0A036 P99136 Q5HHP5 S. aureus Array Staphylococcus aureus 9-Jun-11 Consensus sa_c8986s7896 sp|P09124|G3P1_BACSU Glyceraldehyde 3-phosphate dehydrogenase 1 (GAPDH) (NAD-dependent glyceraldehyde-3-phosphate dehydrogenase) [] match=29.47% identical sa_c8986s7896 --- --- --- --- --- 0006006 // glucose metabolic process // inferred from electronic annotation /// 0006096 // glycolysis // inferred from electronic annotation /// 0008152 // metabolic process // inferred from electronic annotation /// 0055114 // oxidation reduction // inferred from electronic annotation 0005737 // cytoplasm // inferred from electronic annotation 0003824 // catalytic activity // inferred from electronic annotation /// 0004365 // glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity // inferred from electronic annotation /// 0005488 // binding // inferred from electronic annotation /// 0008943 // glyceraldehyde-3-phosphate dehydrogenase activity // inferred from electronic annotation /// 0016491 // oxidoreductase activity // inferred from electronic annotation /// 0051287 // NAD or NADH binding // inferred from electronic annotation This probe set was annotated using the Matching Probes based pipeline to a GenBank identifier using 1 transcripts. // false // Matching Probes // A

Total number of rows: 7775

Table truncated, full table size 4111 Kbytes.






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