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Platform GPL198 Query DataSets for GPL198
Status Public on Jul 18, 2002
Title [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array
Technology type in situ oligonucleotide
Distribution commercial
Organism Arabidopsis thaliana
Manufacturer Affymetrix
Manufacture protocol see manufacturer's web site

The current release has 22810 entries and was indexed 26-Jun-2003.
Annotation data from TAIR, Gene Ontology Consortium and TIGR were mapped to the Arabidopsis ATH1 Array probe sets. The AGI (Arabidopsis Genome Initiative) ID (e.g. AT5G23000) corresponding to the gene represented on the array was used to map annotation data obtained from TAIR, Gene Ontology and TIGR databases. Similarly, gene title and gene symbol, as well as the EC annotations for the AGI ID were extracted from the TIGR database. These annotation mappings were validated by a two-pronged approach. First, probe sets were randomly selected and manually curated to check for consistency between Gene Ontology terms, gene title and protein domain associations. Furthermore, associations within and between data sets from different public databases were also used to check for consistencies. For example, consider the association of gene ontology terms and InterPro IDs. Several Gene Onoltogy terms have InterPro ID(s) curated as supporting evidence for assigning the term to an AGI locus. This relationship was used to validate the consistency of the ontology terms from Gene Onotlogy and InterPro domain annotations from TAIR. The GeneChip® Arabidopsis ATH1 Genome Array contains more than 22,500 probe sets representing approximately 24,000 genes. Sequences used in the design were selected and clustered in collaboration with TIGR and were derived from TIGR's ATH1-121501 Database. Oligoneuclotide probes are synthesized in situ to each corresponding sequence. Eleven pairs of oligoneuclotide probes are used to measure the level of transcription of each sequence represented on the GeneChip Arabidopsis ATH1 Genome Array. Most sequences represented on the previous generation GeneChip® Arabidopsis Genome Array are also represented on the ATH1 array. Due to the dynamic nature of public databases, probe sets for these sequences will not be identical and in some cases will be represented by a completely new probe set. As a result, data generated with different versions of the Arabidopsis array may not always produce concordant results. The probe arrays are for research use only and not intended for use in diagnosis of diseases.

 
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
June 07, 2012: annotation table updated with netaffx build 32
July 01, 2016: annotation table updated with netaffx build 35
 
Web link http://www.affymetrix.com/support/technical/byproduct.affx?product=arab
http://www.affymetrix.com/analysis/index.affx
Submission date Jul 01, 2002
Last update date Jun 12, 2017
Organization Affymetrix, Inc.
E-mail 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 (14219) GSM6227, GSM6544, GSM6571, GSM6572, GSM6573, GSM6574 
Series (1089)
GSE431 pmr4 vs. wild-type (May, 2003)
GSE518 Activation-tagged jaw-d mutant plants
GSE537 Seedling ethylene treatment
Relations
Alternative to GPL8455 (Alternative CDF)
Alternative to GPL10050 (Alternative CDF)
Alternative to GPL10948 (Alternative CDF)
Alternative to GPL10868 (Alternative CDF)
Alternative to GPL13230 (Alternative CDF [ATH1-121501.TAIR9])
Alternative to GPL13838 (Alternative CDF [Brainarray TAIRG, V.12.1.0])
Affiliated with GPL16112 (Alternative CDF [ATH1121501_At_TAIRG, v14.0.0])
Affiliated with GPL18395 (Alternative CDF [Lepidium_LsRNA_FDRp01_ANOVA_Probes_Keep_3probe])
Alternative to GPL21063 (Alternative CDF [ATH1121501_At_TAIRG, v18.0.0])

Data table header descriptions
ID Affymetrix Probe Set ID
ORF Entrez Gene Link
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 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.
AGI TAIR locus tag
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 ORF 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 AGI Gene Ontology Biological Process Gene Ontology Cellular Component Gene Ontology Molecular Function
244901_at orf25 Arabidopsis thaliana Oct 6, 2014 Exemplar sequence Affymetrix Proprietary Database hypothetical protein orf25 unknown protein ORF25 814597 ATMG00640 0006754 // ATP biosynthetic process // inferred from electronic annotation /// 0006810 // transport // inferred from electronic annotation /// 0006811 // ion transport // inferred from electronic annotation /// 0009451 // RNA modification // inferred from electronic annotation /// 0015986 // ATP synthesis coupled proton transport // inferred from electronic annotation /// 0015992 // proton transport // inferred from electronic annotation 0000276 // mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) // inferred from electronic annotation /// 0005739 // mitochondrion // inferred from electronic annotation /// 0005753 // mitochondrial proton-transporting ATP synthase complex // inferred from direct assay /// 0016020 // membrane // inferred from electronic annotation /// 0016021 // integral component of membrane // inferred from electronic annotation /// 0031966 // mitochondrial membrane // inferred from electronic annotation /// 0045263 // proton-transporting ATP synthase complex, coupling factor F(o) // inferred from electronic annotation 0008270 // zinc ion binding // inferred from direct assay /// 0015078 // hydrogen ion transmembrane transporter activity // inferred from electronic annotation /// 0046933 // proton-transporting ATP synthase activity, rotational mechanism // traceable author statement
244902_at nad4L Arabidopsis thaliana Oct 6, 2014 Exemplar sequence Affymetrix Proprietary Database NADH dehydrogenase subunit 4L nad4L unknown protein NAD4L 814598 ATMG00650 0009451 // RNA modification // inferred from electronic annotation /// 0015979 // photosynthesis // RCA /// 0042773 // ATP synthesis coupled electron transport // inferred from electronic annotation /// 0045333 // cellular respiration // traceable author statement /// 0045333 // cellular respiration // RCA /// 0055114 // oxidation-reduction process // inferred from electronic annotation 0005739 // mitochondrion // inferred from electronic annotation /// 0016020 // membrane // inferred from electronic annotation /// 0016021 // integral component of membrane // inferred from electronic annotation /// 0031966 // mitochondrial membrane // inferred from electronic annotation /// 0045271 // respiratory chain complex I // traceable author statement /// 0070469 // respiratory chain // inferred from electronic annotation 0003954 // NADH dehydrogenase activity // traceable author statement /// 0008137 // NADH dehydrogenase (ubiquinone) activity // inferred from electronic annotation /// 0016491 // oxidoreductase activity // inferred from electronic annotation /// 0016651 // oxidoreductase activity, acting on NAD(P)H // inferred from electronic annotation
244903_at orf149 Arabidopsis thaliana Oct 6, 2014 Exemplar sequence Affymetrix Proprietary Database hypothetical protein orf149 hypothetical protein ArthMp059 3371309 0005739 // mitochondrion // inferred from electronic annotation
244904_at orf275 Arabidopsis thaliana Oct 6, 2014 Exemplar sequence Affymetrix Proprietary Database hypothetical protein orf275 hypothetical protein ArthMp060 3371310 0005739 // mitochondrion // inferred from electronic annotation /// 0016020 // membrane // inferred from electronic annotation /// 0016021 // integral component of membrane // inferred from electronic annotation /// 0031966 // mitochondrial membrane // inferred from electronic annotation
244905_at orf122c Arabidopsis thaliana Oct 6, 2014 Exemplar sequence Affymetrix Proprietary Database hypothetical protein orf122c hypothetical protein ArthMp061 4024957 0005739 // mitochondrion // inferred from electronic annotation
244906_at orf240a Arabidopsis thaliana Oct 6, 2014 Exemplar sequence Affymetrix Proprietary Database hypothetical protein orf240a unknown protein ORF240A 4024983 ATMG00690 0009451 // RNA modification // inferred from electronic annotation 0005739 // mitochondrion // inferred from electronic annotation /// 0016020 // membrane // inferred from electronic annotation /// 0016021 // integral component of membrane // inferred from electronic annotation /// 0031966 // mitochondrial membrane // inferred from electronic annotation
244907_at orf120 Arabidopsis thaliana Oct 6, 2014 Exemplar sequence Affymetrix Proprietary Database hypothetical protein orf120 hypothetical protein ArthMp063 4024984 0005739 // mitochondrion // inferred from electronic annotation 0003676 // nucleic acid binding // inferred from electronic annotation
244908_at orf107d Arabidopsis thaliana Oct 6, 2014 Exemplar sequence Affymetrix Proprietary Database hypothetical protein orf107d hypothetical protein ArthMp064 4024985 0005739 // mitochondrion // inferred from electronic annotation
244909_at orf100a Arabidopsis thaliana Oct 6, 2014 Exemplar sequence Affymetrix Proprietary Database hypothetical protein orf100a hypothetical protein ArthMp066 4024986 0005739 // mitochondrion // inferred from electronic annotation
244910_s_at orf119 Arabidopsis thaliana Oct 6, 2014 Exemplar sequence Affymetrix Proprietary Database hypothetical protein orf119 hypothetical protein ArthMp067 4024987 0005739 // mitochondrion // inferred from electronic annotation
244911_at orf170 Arabidopsis thaliana Oct 6, 2014 Exemplar sequence Affymetrix Proprietary Database hypothetical protein orf170 hypothetical protein ArthMp071 4024991 0005739 // mitochondrion // inferred from electronic annotation
244912_at ccb382 Arabidopsis thaliana Oct 6, 2014 Exemplar sequence Affymetrix Proprietary Database cytochrome c biogenesis orf382 Protein sequence is in conflict with the conceptual translation ccb382 cytochrome c biogenesis orf382 ccb382 3890472 AT2G07783 0006461 // protein complex assembly // inferred from electronic annotation /// 0008535 // respiratory chain complex IV assembly // inferred from electronic annotation /// 0009451 // RNA modification // inferred from electronic annotation /// 0015886 // heme transport // inferred from electronic annotation /// 0017004 // cytochrome complex assembly // inferred from electronic annotation 0005739 // mitochondrion // inferred from electronic annotation /// 0016020 // membrane // inferred from electronic annotation /// 0016021 // integral component of membrane // inferred from electronic annotation /// 0031966 // mitochondrial membrane // inferred from electronic annotation 0005515 // protein binding // inferred from physical interaction /// 0015232 // heme transporter activity // inferred from electronic annotation
244913_at orf121b Arabidopsis thaliana Oct 6, 2014 Exemplar sequence Affymetrix Proprietary Database hypothetical protein orf121b hypothetical protein ArthMp073 4024992 0005739 // mitochondrion // inferred from electronic annotation
244914_at orf107e Arabidopsis thaliana Oct 6, 2014 Exemplar sequence Affymetrix Proprietary Database hypothetical protein orf107e hypothetical protein ArthMp074 4024993 0005739 // mitochondrion // inferred from electronic annotation
244915_s_at orf158 Arabidopsis thaliana Oct 6, 2014 Exemplar sequence Affymetrix Proprietary Database hypothetical protein orf158 hypothetical protein ArthMp075 4024994 0005739 // mitochondrion // inferred from electronic annotation
244916_at orf187 Arabidopsis thaliana Oct 6, 2014 Exemplar sequence Affymetrix Proprietary Database hypothetical protein orf187 unknown protein ORF187 4024995 ATMG00880 0005634 // nucleus // ISM /// 0005739 // mitochondrion // inferred from electronic annotation
244917_at orf184 Arabidopsis thaliana Oct 6, 2014 Exemplar sequence Affymetrix Proprietary Database hypothetical protein orf184 hypothetical protein ArthMp076 4024996 0005739 // mitochondrion // inferred from electronic annotation
244918_at orf106d Arabidopsis thaliana Oct 6, 2014 Exemplar sequence Affymetrix Proprietary Database hypothetical protein orf106d hypothetical protein ArthMp078 4024997 0005739 // mitochondrion // inferred from electronic annotation
244919_at ccb203 Arabidopsis thaliana Oct 6, 2014 Exemplar sequence Affymetrix Proprietary Database cytochrome c biogenesis orf203 Protein sequence is in conflict with the conceptual translation ccb203 unknown protein CCB203 3890474 AT2G07768 ATMG00960 0006461 // protein complex assembly // inferred from electronic annotation /// 0008535 // respiratory chain complex IV assembly // inferred from electronic annotation /// 0009451 // RNA modification // inferred from electronic annotation /// 0015886 // heme transport // inferred from electronic annotation /// 0017004 // cytochrome complex assembly // inferred from electronic annotation 0005739 // mitochondrion // not recorded /// 0005739 // mitochondrion // inferred from electronic annotation /// 0005743 // mitochondrial inner membrane // inferred from direct assay /// 0016020 // membrane // inferred from electronic annotation /// 0016021 // integral component of membrane // inferred from electronic annotation /// 0031966 // mitochondrial membrane // inferred from electronic annotation /// 0043234 // protein complex // inferred from direct assay 0005515 // protein binding // inferred from physical interaction /// 0015232 // heme transporter activity // inferred from electronic annotation
244920_s_at nad3 Arabidopsis thaliana Oct 6, 2014 Exemplar sequence Affymetrix Proprietary Database NADH dehydrogenase subunit 3 Protein sequence is in conflict with the conceptual translation nad3 NADH dehydrogenase subunit 3 /// NADH-ubiquinone oxidoreductase chain 3 ArthMp086 /// AT2G07751 815347 3890475 NM_147270 AT2G07751 0006120 // mitochondrial electron transport, NADH to ubiquinone // inferred from sequence or structural similarity /// 0009451 // RNA modification // inferred from electronic annotation /// 0055114 // oxidation-reduction process // inferred from electronic annotation 0005739 // mitochondrion // not recorded /// 0016020 // membrane // inferred from electronic annotation /// 0016021 // integral component of membrane // inferred from electronic annotation /// 0031966 // mitochondrial membrane // inferred from electronic annotation /// 0070469 // respiratory chain // inferred from electronic annotation 0008137 // NADH dehydrogenase (ubiquinone) activity // inferred from sequence or structural similarity /// 0016491 // oxidoreductase activity // inferred from electronic annotation /// 0016651 // oxidoreductase activity, acting on NAD(P)H // inferred from electronic annotation

Total number of rows: 22810

Table truncated, full table size 21395 Kbytes.






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