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Platform GPL89 Query DataSets for GPL89
Status Public on Mar 11, 2002
Title [RT_U34] Affymetrix Rat Toxicology U34 Array
Technology type in situ oligonucleotide
Distribution commercial
Organism Rattus norvegicus
Manufacturer Affymetrix
Manufacture protocol see manufacturer's web site
 
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

Has 1031 entries and was indexed 29-Jan-2002
Contains a relevant set of toxicology genes selected from published scientific literature and in collaboration with pharmaceutical toxicologists.
Includes probes for >850 genes and EST clusters selected from Build 34 of the UniGene database.
Specific full-length sequences were selected based on their known relevance to a toxic or stress-related response. EST clusters were selected basedon their homology to these known genes. UniGene clusters are analyzed by an exemplar sequence that is the most complete and most 3' sequence in the cluster.

Keywords = high density oligonucleotide array
 
Web link http://www.affymetrix.com/support/technical/byproduct.affx?product=rtu34
http://www.affymetrix.com/analysis/index.affx
Submission date Feb 19, 2002
Last update date Jun 03, 2009
Organization Affymetrix, Inc.
E-mail(s) geo@ncbi.nlm.nih.gov, support@affymetrix.com
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 (16) GSM1654, GSM1655, GSM1656, GSM1657, GSM1658, GSM1659 
Series (1)
GSE39 Mefloquine treatment of NG108 rat neuronal cells

Data table header descriptions
ID Affymetrix Probe Set ID
GB_ACC GenBank Accession Number
SPOT_ID
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.
Sequence Source The database from which the sequence used to design this probe set was taken.
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.
Gene Title Title of Gene represented by the probe set.
Gene Symbol A gene symbol, when one is available (from UniGene).
ENTREZ_GENE_ID Entrez Gene Database UID
RefSeq Transcript ID References to multiple sequences in RefSeq. The field contains the ID and Description for each entry, and there can be multiple entries per ProbeSet.
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".

Data table
ID GB_ACC SPOT_ID Species Scientific Name Annotation Date Sequence Type Sequence Source Target Description Representative Public ID Gene Title Gene Symbol ENTREZ_GENE_ID RefSeq Transcript ID Gene Ontology Biological Process Gene Ontology Cellular Component Gene Ontology Molecular Function
AA108277_at AA108277 Rattus norvegicus Mar 11, 2009 Exemplar sequence GenBank AA108277 EST0020 rat lambda ZAPII library (C.P.Hamel) Rattus norvegicus cDNA clone pCO100 5' similar to Heat shock protein (hsp-E7I), mRNA sequence [Rattus norvegicus] AA108277 heat shock 105kDa/110kDa protein 1 Hsph1 288444 NM_001011901 0006950 // response to stress // inferred from electronic annotation /// 0051085 // chaperone cofactor-dependent protein folding // inferred from sequence or structural similarity 0005737 // cytoplasm // inferred from electronic annotation 0000166 // nucleotide binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from sequence or structural similarity /// 0005524 // ATP binding // inferred from electronic annotation
AA108308_i_at AA108308 Rattus norvegicus Mar 11, 2009 Exemplar sequence GenBank AA108308 EST0051 rat lambda ZAPII library (C.P.Hamel) Rattus norvegicus cDNA clone pCO97 5' similar to DNA-binding protein mdm2, mRNA sequence [Rattus norvegicus] AA108308 Mdm2 p53 binding protein homolog (mouse) Mdm2 314856 NM_001108099 /// XM_001080981 /// XM_235169 0000122 // negative regulation of transcription from RNA polymerase II promoter // inferred from sequence or structural similarity /// 0006461 // protein complex assembly // inferred from sequence or structural similarity /// 0007089 // traversing start control point of mitotic cell cycle // inferred from sequence or structural similarity /// 0016567 // protein ubiquitination // inferred from sequence or structural similarity /// 0030163 // protein catabolic process // inferred from sequence or structural similarity /// 0042176 // regulation of protein catabolic process // inferred from sequence or structural similarity /// 0045787 // positive regulation of cell cycle // inferred from sequence or structural similarity 0005626 // insoluble fraction // inferred from sequence or structural similarity /// 0005634 // nucleus // inferred from sequence or structural similarity /// 0005654 // nucleoplasm // inferred from sequence or structural similarity /// 0005730 // nucleolus // inferred from sequence or structural similarity /// 0005737 // cytoplasm // inferred from sequence or structural similarity /// 0005829 // cytosol // inferred from sequence or structural similarity 0002039 // p53 binding // inferred from sequence or structural similarity /// 0004842 // ubiquitin-protein ligase activity // inferred from sequence or structural similarity /// 0005515 // protein binding // inferred from sequence or structural similarity /// 0008270 // zinc ion binding // inferred from sequence or structural similarity /// 0017163 // negative regulator of basal transcription activity // inferred from sequence or structural similarity /// 0019899 // enzyme binding // inferred from sequence or structural similarity /// 0042802 // identical protein binding // inferred from sequence or structural similarity
AA108308_s_at AA108308 Rattus norvegicus Mar 11, 2009 Exemplar sequence GenBank AA108308 EST0051 rat lambda ZAPII library (C.P.Hamel) Rattus norvegicus cDNA clone pCO97 5' similar to DNA-binding protein mdm2, mRNA sequence [Rattus norvegicus] AA108308 Mdm2 p53 binding protein homolog (mouse) Mdm2 314856 NM_001108099 /// XM_001080981 /// XM_235169 0000122 // negative regulation of transcription from RNA polymerase II promoter // inferred from sequence or structural similarity /// 0006461 // protein complex assembly // inferred from sequence or structural similarity /// 0007089 // traversing start control point of mitotic cell cycle // inferred from sequence or structural similarity /// 0016567 // protein ubiquitination // inferred from sequence or structural similarity /// 0030163 // protein catabolic process // inferred from sequence or structural similarity /// 0042176 // regulation of protein catabolic process // inferred from sequence or structural similarity /// 0045787 // positive regulation of cell cycle // inferred from sequence or structural similarity 0005626 // insoluble fraction // inferred from sequence or structural similarity /// 0005634 // nucleus // inferred from sequence or structural similarity /// 0005654 // nucleoplasm // inferred from sequence or structural similarity /// 0005730 // nucleolus // inferred from sequence or structural similarity /// 0005737 // cytoplasm // inferred from sequence or structural similarity /// 0005829 // cytosol // inferred from sequence or structural similarity 0002039 // p53 binding // inferred from sequence or structural similarity /// 0004842 // ubiquitin-protein ligase activity // inferred from sequence or structural similarity /// 0005515 // protein binding // inferred from sequence or structural similarity /// 0008270 // zinc ion binding // inferred from sequence or structural similarity /// 0017163 // negative regulator of basal transcription activity // inferred from sequence or structural similarity /// 0019899 // enzyme binding // inferred from sequence or structural similarity /// 0042802 // identical protein binding // inferred from sequence or structural similarity
AA684537_at AA684537 Rattus norvegicus Mar 11, 2009 Exemplar sequence GenBank AA684537 EST104685 Rat PC-12 cells, untreated Rattus sp. cDNA clone RPCAA05 5' end similar to NADH-ubiquinone oxidoreductase SGDH subunit, mRNA sequence [Rattus sp.] AA684537 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5 Ndufb5 294964 NM_001106426 /// XM_001066565 /// XM_215544 0005739 // mitochondrion // inferred from sequence or structural similarity /// 0005743 // mitochondrial inner membrane // inferred from sequence or structural similarity
AA684929_f_at AA684929 Rattus norvegicus Mar 11, 2009 Exemplar sequence GenBank AA684929 EST105793 Rat PC-12 cells, untreated Rattus sp. cDNA clone RPCAS27 5' end similar to NADH-ubiquinone oxidoreductase, MLRQ subunit, mRNA sequence [Rattus sp.] AA684929
AA684960_f_at AA684960 Rattus norvegicus Mar 11, 2009 Exemplar sequence GenBank AA684960 EST105866 Rat PC-12 cells, untreated Rattus sp. cDNA clone RPCAT93 5' end similar to NADH-ubiquinone oxidoreductase, MLRQ subunit, mRNA sequence [Rattus sp.] AA684960
AA684963_at AA684963 Rattus norvegicus Mar 11, 2009 Exemplar sequence GenBank AA684963 EST105871 Rat PC-12 cells, untreated Rattus sp. cDNA clone RPCAU48 5' end similar to FK506-binding protein, mRNA sequence [Rattus sp.] AA684963 FK506 binding protein 2 Fkbp2 293702 NM_001134428 /// NM_001134429 /// XM_001072401 /// XM_215196 0006457 // protein folding // inferred from electronic annotation 0005515 // protein binding // inferred from sequence or structural similarity
AA685112_at AA685112 Rattus norvegicus Mar 11, 2009 Exemplar sequence GenBank AA685112 EST106280 Rat PC-12 cells, untreated Rattus sp. cDNA clone RPCAZ02 5' end similar to NADH-ubiquinone oxidoreductase complex I 23 kDa precursor (iron-sulfur protein), mRNA sequence [Rattus sp.] AA685112 NADH dehydrogenase (ubiquinone) Fe-S protein 8 Ndufs8 293652 NM_001106322 /// XM_001069669 /// XM_215197 0006979 // response to oxidative stress // inferred from sequence or structural similarity /// 0032981 // mitochondrial respiratory chain complex I assembly // inferred from sequence or structural similarity 0005739 // mitochondrion // inferred from sequence or structural similarity /// 0005747 // mitochondrial respiratory chain complex I // inferred from sequence or structural similarity 0003954 // NADH dehydrogenase activity // inferred from sequence or structural similarity /// 0008137 // NADH dehydrogenase (ubiquinone) activity // inferred from sequence or structural similarity /// 0009055 // electron carrier activity // inferred from electronic annotation /// 0016491 // oxidoreductase activity // inferred from electronic annotation /// 0016651 // oxidoreductase activity, acting on NADH or NADPH // inferred from electronic annotation /// 0051536 // iron-sulfur cluster binding // inferred from electronic annotation
AA685152_r_at AA685152 Rattus norvegicus Mar 11, 2009 Exemplar sequence GenBank AA685152 EST106386 Rat PC-12 cells, untreated Rattus sp. cDNA 5' end similar to Ubiquitin-like protein NEDD-8, mRNA sequence [Rattus sp.] AA685152 neural precursor cell expressed, developmentally down-regulated 8 Nedd8 25490 NM_138878 0006357 // regulation of transcription from RNA polymerase II promoter // inferred from sequence or structural similarity /// 0006464 // protein modification process // inferred from electronic annotation /// 0006511 // ubiquitin-dependent protein catabolic process // inferred from electronic annotation /// 0008104 // protein localization // inferred from sequence or structural similarity /// 0014070 // response to organic cyclic substance // inferred from direct assay /// 0045116 // protein neddylation // inferred from direct assay /// 0045116 // protein neddylation // inferred from sequence or structural similarity 0005634 // nucleus // inferred from direct assay /// 0005634 // nucleus // inferred from electronic annotation /// 0005634 // nucleus // inferred from sequence or structural similarity 0005515 // protein binding // inferred from direct assay /// 0005515 // protein binding // inferred from sequence or structural similarity
AA685376_f_at AA685376 Rattus norvegicus Mar 11, 2009 Exemplar sequence GenBank AA685376 EST107010 Rat PC-12 cells, untreated Rattus sp. cDNA clone RPCBJ78 5' end similar to NADH-ubiquinone oxidoreductase, MLRQ subunit, mRNA sequence [Rattus sp.] AA685376
AA685876_at AA685876 Rattus norvegicus Mar 11, 2009 Exemplar sequence GenBank AA685876 EST108473 Rat PC-12 cells, NGF-treated (9 days) Rattus sp. cDNA clone RPNAA25 5' end similar to NADH-cytochrome b5 reductase, mRNA sequence [Rattus sp.] AA685876 cytochrome b5 reductase 1 Cyb5r1 304805 NM_001013126 0006694 // steroid biosynthetic process // inferred from electronic annotation /// 0008610 // lipid biosynthetic process // inferred from electronic annotation /// 0016126 // sterol biosynthetic process // inferred from electronic annotation /// 0055114 // oxidation reduction // inferred from electronic annotation 0005730 // nucleolus // inferred from sequence or structural similarity /// 0005737 // cytoplasm // inferred from sequence or structural similarity /// 0016020 // membrane // inferred from electronic annotation /// 0016021 // integral to membrane // inferred from electronic annotation 0004128 // cytochrome-b5 reductase activity // inferred from electronic annotation /// 0009055 // electron carrier activity // inferred from electronic annotation /// 0016491 // oxidoreductase activity // inferred from electronic annotation
AA685903_at AA685903 Rattus norvegicus Mar 11, 2009 Exemplar sequence GenBank AA685903 EST108576 Rat PC-12 cells, NGF-treated (9 days) Rattus sp. cDNA clone RPNAC21 5' end similar to Glucose regulated protein, 94 kDa (GRP94), mRNA sequence [Rattus sp.] AA685903 tumor rejection antigen gp96 Tra1 362862 NM_001012197 0006457 // protein folding // inferred from electronic annotation 0005783 // endoplasmic reticulum // inferred from electronic annotation /// 0005788 // endoplasmic reticulum lumen // inferred from electronic annotation /// 0042470 // melanosome // inferred from electronic annotation 0000166 // nucleotide binding // inferred from electronic annotation /// 0005509 // calcium ion binding // inferred from electronic annotation /// 0005524 // ATP binding // inferred from electronic annotation /// 0051082 // unfolded protein binding // inferred from electronic annotation
AA686031_at AA686031 Rattus norvegicus Mar 11, 2009 Exemplar sequence GenBank AA686031 EST109008 Rat PC-12 cells, NGF-treated (9 days) Rattus sp. cDNA clone RPNAJ84 5' end similar to NADH-ubiquinone oxidoreductase 75 kDa subunit, mRNA sequence [Rattus sp.] AA686031 NADH dehydrogenase (ubiquinone) Fe-S protein 1 Ndufs1 301458 NM_001005550 0006800 // oxygen and reactive oxygen species metabolic process // inferred from sequence or structural similarity /// 0006810 // transport // inferred from electronic annotation /// 0006915 // apoptosis // inferred from sequence or structural similarity /// 0022900 // electron transport chain // inferred from electronic annotation /// 0042773 // ATP synthesis coupled electron transport // inferred from electronic annotation /// 0045333 // cellular respiration // inferred from sequence or structural similarity /// 0046034 // ATP metabolic process // inferred from sequence or structural similarity /// 0051881 // regulation of mitochondrial membrane potential // inferred from sequence or structural similarity /// 0055114 // oxidation reduction // inferred from electronic annotation 0005739 // mitochondrion // inferred from electronic annotation /// 0005739 // mitochondrion // inferred from sequence or structural similarity /// 0005743 // mitochondrial inner membrane // inferred from electronic annotation /// 0005746 // mitochondrial respiratory chain // inferred from electronic annotation /// 0005747 // mitochondrial respiratory chain complex I // inferred from sequence or structural similarity /// 0005758 // mitochondrial intermembrane space // inferred from sequence or structural similarity /// 0016020 // membrane // inferred from electronic annotation 0003954 // NADH dehydrogenase activity // inferred from electronic annotation /// 0005506 // iron ion binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from sequence or structural similarity /// 0008137 // NADH dehydrogenase (ubiquinone) activity // inferred from sequence or structural similarity /// 0008137 // NADH dehydrogenase (ubiquinone) activity // inferred from electronic annotation /// 0009055 // electron carrier activity // inferred from electronic annotation /// 0016491 // oxidoreductase activity // inferred from electronic annotation /// 0016651 // oxidoreductase activity, acting on NADH or NADPH // inferred from electronic annotation /// 0046872 // metal ion binding // inferred from electronic annotation /// 0051536 // iron-sulfur cluster binding // inferred from electronic annotation /// 0051537 // 2 iron, 2 sulfur cluster binding // inferred from electronic annotation /// 0051539 // 4 iron, 4 sulfur cluster binding // inferred from electronic annotation
AA686579_at AA686579 Rattus norvegicus Mar 11, 2009 Exemplar sequence GenBank AA686579 EST110738 Rat PC-12 cells, NGF-treated (9 days) Rattus sp. cDNA clone RPNBL48 5' end similar to Ubiquitin-like protein NEDD-8, mRNA sequence [Rattus sp.] AA686579 SMT3 suppressor of mif two 3 homolog 1 (S. cerevisiae) Sumo1 301442 NM_001009672 0006464 // protein modification process // inferred from electronic annotation /// 0006511 // ubiquitin-dependent protein catabolic process // inferred from electronic annotation /// 0016481 // negative regulation of transcription // inferred from sequence or structural similarity /// 0016925 // protein sumoylation // inferred from sequence or structural similarity /// 0031334 // positive regulation of protein complex assembly // inferred from sequence or structural similarity /// 0043433 // negative regulation of transcription factor activity // inferred from sequence or structural similarity /// 0045449 // regulation of transcription // inferred from sequence or structural similarity 0005634 // nucleus // inferred from direct assay /// 0005634 // nucleus // inferred from electronic annotation /// 0005634 // nucleus // inferred from sequence or structural similarity /// 0005737 // cytoplasm // inferred from electronic annotation /// 0016605 // PML body // inferred from sequence or structural similarity /// 0030425 // dendrite // inferred from direct assay /// 0045202 // synapse // inferred from direct assay 0005515 // protein binding // inferred from sequence or structural similarity /// 0008134 // transcription factor binding // inferred from sequence or structural similarity /// 0019789 // SUMO ligase activity // inferred from sequence or structural similarity
AA686870_f_at AA686870 Rattus norvegicus Mar 11, 2009 Exemplar sequence GenBank AA686870 EST111576 Rat PC-12 cells, NGF-treated (9 days) Rattus sp. cDNA clone RPNCF62 5' end similar to NADH-ubiquinone oxidoreductase, MLRQ subunit, mRNA sequence [Rattus sp.] AA686870
AA686870_i_at AA686870 Rattus norvegicus Mar 11, 2009 Exemplar sequence GenBank AA686870 EST111576 Rat PC-12 cells, NGF-treated (9 days) Rattus sp. cDNA clone RPNCF62 5' end similar to NADH-ubiquinone oxidoreductase, MLRQ subunit, mRNA sequence [Rattus sp.] AA686870
AA799336_at AA799336 Rattus norvegicus Mar 11, 2009 Exemplar sequence GenBank AA799336 EST188833 Rattus norvegicus cDNA, 5' end /clone=RHEAA38 /clone_end=5' /gb=AA799336 /gi=2862291 /ug=Rn.1318 /len=599 AA799336 NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1 Ndufab1 293453 NM_001106294 /// XM_001079490 /// XM_215044 0006633 // fatty acid biosynthetic process // inferred from electronic annotation 0005739 // mitochondrion // inferred from sequence or structural similarity 0000036 // acyl carrier activity // inferred from electronic annotation /// 0031177 // phosphopantetheine binding // inferred from electronic annotation /// 0048037 // cofactor binding // inferred from electronic annotation
AA819943_at AA819943 Rattus norvegicus Mar 11, 2009 Exemplar sequence GenBank AA819943 EST49a-1 Rat Brain, Stratagene (cat.#936501) Rattus norvegicus cDNA clone pBS/49a-1 3', mRNA sequence [Rattus norvegicus] AA819943
AA848218_at AA848218 Rattus norvegicus Mar 11, 2009 Exemplar sequence GenBank AA848218 EST190978 Normalized rat heart, Bento Soares Rattus sp. cDNA clone RHEAC12 5' end similar to DNA topoisomerase I, mRNA sequence [Rattus sp.] AA848218 Topoisomerase (DNA) I Top1 64550 NM_022615 0006260 // DNA replication // inferred from sequence or structural similarity /// 0006265 // DNA topological change // inferred from direct assay /// 0006265 // DNA topological change // inferred from electronic annotation /// 0006265 // DNA topological change // inferred from sequence or structural similarity /// 0006268 // DNA unwinding during replication // inferred from electronic annotation /// 0040016 // embryonic cleavage // inferred from sequence or structural similarity /// 0042493 // response to drug // inferred from sequence or structural similarity 0005634 // nucleus // inferred from direct assay /// 0005634 // nucleus // inferred from electronic annotation /// 0005634 // nucleus // inferred from sequence or structural similarity /// 0005654 // nucleoplasm // inferred from sequence or structural similarity /// 0005694 // chromosome // inferred from electronic annotation /// 0005694 // chromosome // inferred from sequence or structural similarity /// 0005730 // nucleolus // inferred from sequence or structural similarity /// 0005737 // cytoplasm // inferred from sequence or structural similarity /// 0043204 // perikaryon // inferred from sequence or structural similarity 0003677 // DNA binding // inferred from electronic annotation /// 0003682 // chromatin binding // inferred from sequence or structural similarity /// 0003916 // DNA topoisomerase activity // inferred from electronic annotation /// 0003917 // DNA topoisomerase type I activity // inferred from direct assay /// 0003917 // DNA topoisomerase type I activity // inferred from electronic annotation /// 0003917 // DNA topoisomerase type I activity // inferred from sequence or structural similarity /// 0003918 // DNA topoisomerase (ATP-hydrolyzing) activity // inferred from electronic annotation /// 0005515 // protein binding // inferred from sequence or structural similarity /// 0016853 // isomerase activity // inferred from electronic annotation /// 0031490 // chromatin DNA binding // inferred from direct assay
AA848268_at AA848268 Rattus norvegicus Mar 11, 2009 Exemplar sequence GenBank AA848268 EST191028 Normalized rat heart, Bento Soares Rattus sp. cDNA clone RHEAC66 5' end similar to DnaJ protein homolog 2, mRNA sequence [Rattus sp.] AA848268 DnaJ (Hsp40) homolog, subfamily A, member 4 Dnaja4 300721 NM_001025411 0006457 // protein folding // inferred from electronic annotation 0031072 // heat shock protein binding // inferred from electronic annotation /// 0051082 // unfolded protein binding // inferred from electronic annotation

Total number of rows: 1031

Table truncated, full table size 1937 Kbytes.






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