Array B of GeneChip Rat Expression Set 230 Has 15333 entries and was indexed 09-Apr-2003 Sequences used in the design of the array were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from Build 99 of UniGene (June 2002) and refined by analysis and comparison with a number of other publicly available databases including the Baylor College of Medicine Human Genome Sequencing Center's preliminary rat genome assembly (June 2002). In addition, sequences were analyzed for untrimmed low-quality sequence information, correct orientation, false clustering, alternative splicing and alternative polyadenylation.
Gene expression data from rat cochlear lateral wall after 3NP damage
Data table header descriptions
ID
Affymetrix Probe Set ID
GB_ACC
GenBank Accession Number
SPOT_ID
identifies controls
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
Sequence Source
The database from which the sequence used to design this probe set was taken.
Target Description
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".
0006464 // protein modification process // inferred from electronic annotation /// 0006511 // ubiquitin-dependent protein catabolic process // inferred from electronic annotation /// 0006879 // cellular iron ion homeostasis // inferred from electronic annotation
0005634 // nucleus // inferred from electronic annotation
0008199 // ferric iron binding // inferred from electronic annotation /// 0016491 // oxidoreductase activity // inferred from electronic annotation /// 0046914 // transition metal ion binding // inferred from electronic annotation
0006810 // transport // inferred from electronic annotation /// 0006886 // intracellular protein transport // inferred from electronic annotation /// 0006890 // retrograde vesicle-mediated transport, Golgi to ER // inferred from sequence or structural similarity /// 0006891 // intra-Golgi vesicle-mediated transport // inferred from sequence or structural similarity /// 0015031 // protein transport // inferred from electronic annotation /// 0016044 // membrane organization // inferred from sequence or structural similarity /// 0016192 // vesicle-mediated transport // inferred from electronic annotation /// 0048193 // Golgi vesicle transport // inferred from physical interaction /// 0048205 // COPI coating of Golgi vesicle // inferred from sequence or structural similarity
0000139 // Golgi membrane // inferred from direct assay /// 0000139 // Golgi membrane // inferred from electronic annotation /// 0005737 // cytoplasm // inferred from electronic annotation /// 0005794 // Golgi apparatus // inferred from sequence or structural similarity /// 0005794 // Golgi apparatus // inferred from electronic annotation /// 0005829 // cytosol // inferred from sequence or structural similarity /// 0016020 // membrane // inferred from electronic annotation /// 0030117 // membrane coat // inferred from electronic annotation /// 0030126 // COPI vesicle coat // inferred from sequence or structural similarity /// 0031410 // cytoplasmic vesicle // inferred from electronic annotation
0005080 // protein kinase C binding // inferred from direct assay /// 0005198 // structural molecule activity // inferred from electronic annotation /// 0005515 // protein binding // inferred from direct assay /// 0005515 // protein binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from sequence or structural similarity
0006302 // double-strand break repair // inferred from sequence or structural similarity /// 0006810 // transport // inferred from electronic annotation /// 0006888 // ER to Golgi vesicle-mediated transport // inferred from mutant phenotype /// 0006919 // caspase activation // inferred from sequence or structural similarity /// 0006974 // response to DNA damage stimulus // inferred from sequence or structural similarity /// 0030970 // retrograde protein transport, ER to cytosol // inferred from sequence or structural similarity /// 0043161 // proteasomal ubiquitin-dependent protein catabolic process // inferred from mutant phenotype /// 0051260 // protein homooligomerization // inferred from direct assay
0005634 // nucleus // inferred from electronic annotation /// 0005634 // nucleus // inferred from sequence or structural similarity /// 0005737 // cytoplasm // inferred from electronic annotation /// 0005783 // endoplasmic reticulum // inferred from direct assay /// 0005783 // endoplasmic reticulum // inferred from sequence or structural similarity /// 0005792 // microsome // inferred from direct assay /// 0005792 // microsome // inferred from sequence or structural similarity /// 0005829 // cytosol // inferred from sequence or structural similarity
0000166 // nucleotide binding // inferred from electronic annotation /// 0005488 // binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from direct assay /// 0005515 // protein binding // inferred from physical interaction /// 0005515 // protein binding // inferred from sequence or structural similarity /// 0005524 // ATP binding // inferred from electronic annotation /// 0008289 // lipid binding // inferred from electronic annotation /// 0016787 // hydrolase activity // inferred from electronic annotation /// 0016887 // ATPase activity // inferred from direct assay /// 0017111 // nucleoside-triphosphatase activity // inferred from electronic annotation /// 0019904 // protein domain specific binding // inferred from sequence or structural similarity
0006511 // ubiquitin-dependent protein catabolic process // inferred from direct assay /// 0006511 // ubiquitin-dependent protein catabolic process // inferred from electronic annotation /// 0016567 // protein ubiquitination // inferred from sequence or structural similarity /// 0030509 // BMP signaling pathway // inferred from sequence or structural similarity /// 0043161 // proteasomal ubiquitin-dependent protein catabolic process // inferred from sequence or structural similarity /// 0043687 // post-translational protein modification // inferred from electronic annotation /// 0051246 // regulation of protein metabolic process // inferred from electronic annotation
0004842 // ubiquitin-protein ligase activity // inferred from direct assay /// 0004842 // ubiquitin-protein ligase activity // inferred from electronic annotation /// 0005515 // protein binding // inferred from sequence or structural similarity /// 0016874 // ligase activity // inferred from electronic annotation /// 0019787 // small conjugating protein ligase activity // inferred from electronic annotation
0006810 // transport // inferred from electronic annotation /// 0006890 // retrograde vesicle-mediated transport, Golgi to ER // inferred from sequence or structural similarity /// 0007264 // small GTPase mediated signal transduction // inferred from electronic annotation /// 0015031 // protein transport // inferred from electronic annotation /// 0016044 // membrane organization // inferred from sequence or structural similarity /// 0016192 // vesicle-mediated transport // inferred from electronic annotation /// 0016192 // vesicle-mediated transport // inferred from sequence or structural similarity /// 0048205 // COPI coating of Golgi vesicle // inferred from sequence or structural similarity
0000139 // Golgi membrane // inferred from sequence or structural similarity /// 0005622 // intracellular // inferred from electronic annotation /// 0005794 // Golgi apparatus // inferred from electronic annotation /// 0005794 // Golgi apparatus // inferred from sequence or structural similarity /// 0005829 // cytosol // inferred from sequence or structural similarity /// 0012505 // endomembrane system // inferred from sequence or structural similarity /// 0030017 // sarcomere // inferred from sequence or structural similarity
0000166 // nucleotide binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from sequence or structural similarity /// 0005525 // GTP binding // inferred from electronic annotation
0007264 // small GTPase mediated signal transduction // inferred from sequence or structural similarity /// 0015031 // protein transport // inferred from electronic annotation /// 0015031 // protein transport // traceable author statement /// 0016192 // vesicle-mediated transport // inferred from expression pattern /// 0043087 // regulation of GTPase activity // inferred from electronic annotation
0005737 // cytoplasm // inferred from electronic annotation /// 0005794 // Golgi apparatus // inferred from sequence or structural similarity /// 0005829 // cytosol // traceable author statement /// 0009986 // cell surface // inferred from sequence or structural similarity /// 0016020 // membrane // inferred from electronic annotation
0005093 // Rab GDP-dissociation inhibitor activity // inferred from direct assay /// 0005093 // Rab GDP-dissociation inhibitor activity // inferred from electronic annotation /// 0005096 // GTPase activator activity // inferred from electronic annotation /// 0005097 // Rab GTPase activator activity // inferred from sequence or structural similarity /// 0031267 // small GTPase binding // inferred from direct assay
0006810 // transport // inferred from electronic annotation /// 0006886 // intracellular protein transport // inferred from electronic annotation /// 0006890 // retrograde vesicle-mediated transport, Golgi to ER // inferred from sequence or structural similarity /// 0006890 // retrograde vesicle-mediated transport, Golgi to ER // traceable author statement /// 0006891 // intra-Golgi vesicle-mediated transport // inferred from direct assay /// 0015031 // protein transport // inferred from electronic annotation /// 0016044 // membrane organization // inferred from sequence or structural similarity /// 0016192 // vesicle-mediated transport // inferred from electronic annotation /// 0048205 // COPI coating of Golgi vesicle // inferred from sequence or structural similarity
0000139 // Golgi membrane // inferred from electronic annotation /// 0005737 // cytoplasm // inferred from electronic annotation /// 0005794 // Golgi apparatus // inferred from direct assay /// 0005794 // Golgi apparatus // inferred from sequence or structural similarity /// 0005794 // Golgi apparatus // inferred from electronic annotation /// 0005798 // Golgi-associated vesicle // inferred from direct assay /// 0005829 // cytosol // inferred from sequence or structural similarity /// 0016020 // membrane // inferred from electronic annotation /// 0030117 // membrane coat // inferred from electronic annotation /// 0030126 // COPI vesicle coat // inferred from direct assay /// 0030126 // COPI vesicle coat // inferred from electronic annotation /// 0031410 // cytoplasmic vesicle // inferred from electronic annotation
0005198 // structural molecule activity // inferred from electronic annotation /// 0005488 // binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from direct assay /// 0005515 // protein binding // inferred from sequence or structural similarity /// 0005515 // protein binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from physical interaction
0006350 // transcription // inferred from electronic annotation /// 0006355 // regulation of transcription, DNA-dependent // inferred from electronic annotation
0005634 // nucleus // inferred from sequence or structural similarity /// 0005634 // nucleus // inferred from electronic annotation /// 0005737 // cytoplasm // inferred from electronic annotation /// 0005739 // mitochondrion // inferred from electronic annotation /// 0005739 // mitochondrion // inferred from sequence or structural similarity /// 0005743 // mitochondrial inner membrane // inferred from sequence or structural similarity /// 0005743 // mitochondrial inner membrane // inferred from electronic annotation /// 0016020 // membrane // inferred from electronic annotation
0004872 // receptor activity // inferred from electronic annotation /// 0005515 // protein binding // inferred from sequence or structural similarity /// 0016566 // specific transcriptional repressor activity // inferred from sequence or structural similarity
0001824 // blastocyst development // inferred from sequence or structural similarity /// 0006915 // apoptosis // inferred from electronic annotation /// 0006916 // anti-apoptosis // inferred from sequence or structural similarity /// 0007584 // response to nutrient // inferred from expression pattern /// 0042493 // response to drug // inferred from expression pattern
0016020 // membrane // inferred from electronic annotation /// 0016021 // integral to membrane // inferred from electronic annotation
0004579 // dolichyl-diphosphooligosaccharide-protein glycotransferase activity // inferred from electronic annotation /// 0016740 // transferase activity // inferred from electronic annotation
0016226 // iron-sulfur cluster assembly // inferred from electronic annotation
0005737 // cytoplasm // inferred from sequence or structural similarity /// 0005739 // mitochondrion // inferred from sequence or structural similarity /// 0005829 // cytosol // inferred from sequence or structural similarity
0005506 // iron ion binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from electronic annotation /// 0032947 // protein complex scaffold // inferred from sequence or structural similarity /// 0051536 // iron-sulfur cluster binding // inferred from electronic annotation
0006446 // regulation of translational initiation // inferred from sequence or structural similarity /// 0016070 // RNA metabolic process // inferred from electronic annotation
0005737 // cytoplasm // inferred from sequence or structural similarity /// 0016281 // eukaryotic translation initiation factor 4F complex // inferred from sequence or structural similarity
0003743 // translation initiation factor activity // inferred from sequence or structural similarity /// 0005488 // binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from electronic annotation /// 0005515 // protein binding // inferred from sequence or structural similarity /// 0008135 // translation factor activity, nucleic acid binding // inferred from sequence or structural similarity
0006886 // intracellular protein transport // inferred from electronic annotation /// 0016192 // vesicle-mediated transport // inferred from sequence or structural similarity
0005622 // intracellular // inferred from electronic annotation /// 0005783 // endoplasmic reticulum // inferred from sequence or structural similarity /// 0016529 // sarcoplasmic reticulum // inferred from sequence or structural similarity
0000166 // nucleotide binding // inferred from electronic annotation /// 0005525 // GTP binding // inferred from electronic annotation
0000398 // nuclear mRNA splicing, via spliceosome // inferred from sequence or structural similarity /// 0006350 // transcription // inferred from electronic annotation /// 0006367 // transcription initiation from RNA polymerase II promoter // inferred from sequence or structural similarity /// 0006368 // RNA elongation from RNA polymerase II promoter // inferred from sequence or structural similarity
0005634 // nucleus // inferred from electronic annotation /// 0005654 // nucleoplasm // inferred from sequence or structural similarity
0003677 // DNA binding // inferred from electronic annotation /// 0003899 // DNA-directed RNA polymerase activity // inferred from electronic annotation
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