This GeneChip probe array is a powerful tool for monitoring trascriptional regulation and antimicrobial agent response of P. aeruginosa. The array represents the annotated genome of P. aeruginosa strain PA01 and includes 5,549 protein-coding sequences, 18 tRNA genes, a representative of the ribosomal RNA cluster and 117 genes present in strains other than PA01.
In addition, 199 probe sets corresponding to all intergenic regions exceeding 600 base pairs have been included. The selected probes have been screened against sequence homologies in the existing database of human genes.
Keywords = high density oligonucleotide array July 06, 2016: annotation table updated with netaffx build 35
Analysis of Pseudomonas aeruginosa evolving in the cystic fibrosis lung uncovers limited evidence that mutator lineages are more genetically variable than non-mutator lineages
Ex vivo transcriptional profiling reveals a common set of genes important for the adaptation of Pseudomonas aeruginosa to chronically infected host sites
Expression pattern of Pseudomonas aeruginosa biofilm-residing bacteria exposed to gentamicin or surface acoustic waves or gentamicin and surface acoustic waves combined
Gene expression data from Pseudomonas aeruginosa PAO1 and mutator (Δ mutS) evolved for 940 generations in LB with and without sub-inhibitory concentrations of ciprofloxacin (0.05µg/ml)
The anti-sigma factor MucA of Pseudomonas aeruginosa: dramatic differences of mucA22 vs. DmucA mutants in anaerobic acidified nitrite sensitivity of planktonic and biofilm bacteria in vitro and during chronic murine lung infection
Identification of genes regulated by rpoH in Pseudomonas aeruginosa
Data table header descriptions
ID
Affymetrix Probe Set ID
ORF
Locus tag for NC_002516.1
SPOT_ID
Spot identifier
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
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".
0006007 // glucose catabolic process // inferred from reviewed computational analysis /// 0006094 // gluconeogenesis // inferred from reviewed computational analysis /// 0007010 // cytoskeleton organization // inferred from reviewed computational analysis /// 0007010 // cytoskeleton organization // traceable author statement /// 0009416 // response to light stimulus // inferred from expression pattern /// 0009611 // response to wounding // inferred from expression pattern /// 0009733 // response to auxin // inferred from expression pattern /// 0009845 // seed germination // inferred from mutant phenotype /// 0010053 // root epidermal cell differentiation // inferred from mutant phenotype /// 0010498 // proteasomal protein catabolic process // inferred from reviewed computational analysis /// 0032880 // regulation of protein localization // inferred from reviewed computational analysis /// 0048364 // root development // inferred from mutant phenotype /// 0048767 // root hair elongation // inferred from mutant phenotype /// 0048767 // root hair elongation // inferred from reviewed computational analysis /// 0051301 // cell division // inferred from mutant phenotype
0005618 // cell wall // inferred from direct assay /// 0005730 // nucleolus // inferred from direct assay /// 0005737 // cytoplasm // not recorded /// 0005739 // mitochondrion // inferred from direct assay /// 0005829 // cytosol // inferred from direct assay /// 0005856 // cytoskeleton // inferred from sequence or structural similarity /// 0005886 // plasma membrane // inferred from direct assay /// 0009506 // plasmodesma // inferred from direct assay /// 0009570 // chloroplast stroma // inferred from direct assay /// 0009941 // chloroplast envelope // inferred from direct assay
0000166 // nucleotide binding // inferred from electronic annotation /// 0005200 // structural constituent of cytoskeleton // inferred from sequence or structural similarity /// 0005515 // protein binding // inferred from physical interaction /// 0005524 // ATP binding // inferred from electronic annotation
M64116 Arabidopsis thaliana glyceraldehyde 3-phosphate dehydrogenase C subunit (GapC) gene
M64116
glyceraldehyde-3-phosphate dehydrogenase C subunit 1
GAPC1
819567
NM_111283
0006006 // glucose metabolic process // inferred from electronic annotation /// 0006007 // glucose catabolic process // inferred from reviewed computational analysis /// 0006094 // gluconeogenesis // inferred from reviewed computational analysis /// 0006094 // gluconeogenesis // traceable author statement /// 0006096 // glycolytic process // inferred from direct assay /// 0006096 // glycolytic process // inferred from sequence or structural similarity /// 0006096 // glycolytic process // inferred from reviewed computational analysis /// 0006096 // glycolytic process // traceable author statement /// 0006098 // pentose-phosphate shunt // inferred from reviewed computational analysis /// 0006833 // water transport // inferred from reviewed computational analysis /// 0006950 // response to stress // inferred from electronic annotation /// 0006972 // hyperosmotic response // inferred from reviewed computational analysis /// 0006979 // response to oxidative stress // inferred from direct assay /// 0006979 // response to oxidative stress // inferred from expression pattern /// 0007010 // cytoskeleton organization // inferred from reviewed computational analysis /// 0007030 // Golgi organization // inferred from reviewed computational analysis /// 0009060 // aerobic respiration // inferred from reviewed computational analysis /// 0009266 // response to temperature stimulus // inferred from reviewed computational analysis /// 0009408 // response to heat // inferred from expression pattern /// 0009651 // response to salt stress // inferred from expression pattern /// 0009651 // response to salt stress // inferred from reviewed computational analysis /// 0009744 // response to sucrose // inferred from expression pattern /// 0010154 // fruit development // inferred from mutant phenotype /// 0010498 // proteasomal protein catabolic process // inferred from reviewed computational analysis /// 0034976 // response to endoplasmic reticulum stress // inferred from reviewed computational analysis /// 0042542 // response to hydrogen peroxide // inferred from direct assay /// 0046686 // response to cadmium ion // inferred from expression pattern /// 0046686 // response to cadmium ion // inferred from reviewed computational analysis /// 0048316 // seed development // inferred from mutant phenotype /// 0051775 // response to redox state // inferred from direct assay /// 0055114 // oxidation-reduction process // inferred from electronic annotation
0005634 // nucleus // inferred from direct assay /// 0005737 // cytoplasm // not recorded /// 0005739 // mitochondrion // inferred from direct assay /// 0005740 // mitochondrial envelope // inferred from direct assay /// 0005774 // vacuolar membrane // inferred from direct assay /// 0005794 // Golgi apparatus // inferred from reviewed computational analysis /// 0005829 // cytosol // inferred from direct assay /// 0005829 // cytosol // traceable author statement /// 0005886 // plasma membrane // inferred from direct assay /// 0009507 // chloroplast // inferred from direct assay /// 0016020 // membrane // inferred from direct assay /// 0048046 // apoplast // inferred from direct assay
0003677 // DNA binding // inferred from electronic annotation /// 0004365 // glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity // traceable author statement /// 0005507 // copper ion binding // inferred from direct assay /// 0008886 // glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity // inferred from direct assay /// 0016491 // oxidoreductase activity // inferred from electronic annotation /// 0016620 // oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor // inferred from electronic annotation /// 0050661 // NADP binding // inferred from electronic annotation /// 0051287 // NAD binding // inferred from electronic annotation
0000278 // mitotic cell cycle // inferred from direct assay /// 0006486 // protein glycosylation // inferred from electronic annotation /// 0006487 // protein N-linked glycosylation // inferred from physical interaction /// 0007049 // cell cycle // inferred from direct assay /// 0018279 // protein N-linked glycosylation via asparagine // inferred from electronic annotation
0005635 // nuclear envelope // inferred from direct assay /// 0005783 // endoplasmic reticulum // inferred from direct assay /// 0005783 // endoplasmic reticulum // inferred from electronic annotation /// 0005789 // endoplasmic reticulum membrane // inferred from electronic annotation /// 0005789 // endoplasmic reticulum membrane // inferred from mutant phenotype /// 0008250 // oligosaccharyltransferase complex // inferred from physical interaction /// 0016020 // membrane // inferred from electronic annotation /// 0016021 // integral component of membrane // inferred from electronic annotation
0004579 // dolichyl-diphosphooligosaccharide-protein glycotransferase activity // inferred from electronic annotation /// 0016740 // transferase activity // inferred from electronic annotation /// 0016757 // transferase activity, transferring glycosyl groups // inferred from electronic annotation
0006122 // mitochondrial electron transport, ubiquinol to cytochrome c // inferred from direct assay /// 0009060 // aerobic respiration // inferred from mutant phenotype /// 0055114 // oxidation-reduction process // inferred from electronic annotation /// 1902600 // hydrogen ion transmembrane transport // inferred from electronic annotation
0005739 // mitochondrion // inferred from direct assay /// 0005739 // mitochondrion // inferred from electronic annotation /// 0005739 // mitochondrion // inferred from physical interaction /// 0005743 // mitochondrial inner membrane // inferred from electronic annotation /// 0005750 // mitochondrial respiratory chain complex III // inferred from direct assay /// 0016020 // membrane // inferred from electronic annotation /// 0016021 // integral component of membrane // inferred from electronic annotation /// 0070469 // respiratory chain // inferred from electronic annotation
0008121 // ubiquinol-cytochrome-c reductase activity // inferred from electronic annotation /// 0016491 // oxidoreductase activity // inferred from electronic annotation /// 0016679 // oxidoreductase activity, acting on diphenols and related substances as donors // 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
L12026 SGD:YER022W S. cerevisiae SRB4 RNA polymerase II holoenzyme/mediator subunit
YER022W
Srb4p
SRB4
856743
NM_001178913
0006351 // transcription, DNA-templated // inferred from electronic annotation /// 0006355 // regulation of transcription, DNA-templated // inferred from electronic annotation /// 0006357 // regulation of transcription from RNA polymerase II promoter // inferred from electronic annotation /// 0006367 // transcription initiation from RNA polymerase II promoter // inferred from mutant phenotype /// 0045944 // positive regulation of transcription from RNA polymerase II promoter // inferred from direct assay
0005634 // nucleus // inferred from electronic annotation /// 0016592 // mediator complex // inferred from electronic annotation /// 0070847 // core mediator complex // inferred from direct assay
0001104 // RNA polymerase II transcription cofactor activity // inferred from electronic annotation /// 0001139 // core RNA polymerase II recruiting transcription factor activity // inferred from mutant phenotype /// 0001139 // core RNA polymerase II recruiting transcription factor activity // inferred from physical interaction /// 0005198 // structural molecule activity // inferred from mutant phenotype /// 0033613 // activating transcription factor binding // inferred from direct assay
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