Has 7312 entries and was indexed 29-Jan-2002. Contains probes for more than 4,200 known open reading frames of E. coli. Also contains probe sets for stable RNA species as well as intergenic regions that do not correspond to known ORFs. Sequence information for probes corresponds to the M54 version of E. coli Genome Project database at the University of Wisconsin. Sequences corresponding to both characterized genes and those whose function is unknown can be identified according to the numbering convention used by the E. coli Genome Project database. Keywords = high density oligonucleotide array
Cisplatin-induced gene expression in DNA adenine methyltransferase (dam) and mismatch repair deficient E. coli
Data table header descriptions
ID
Affymetrix Probe Set ID
ORF
Locus tag
SPOT_ID
identifies controls and intergenic regions
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
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".
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