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Platform GPL8455 Query DataSets for GPL8455
Status Public on Jun 02, 2009
Title [ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array - custom CDF (tinesath1cdf)
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Arabidopsis thaliana
Manufacturer Affymetrix
Manufacture protocol see manufacturer's web site
 
Description see manufacturer's web site/ data processing:an alternative CDF ("tinesath1cdf") was used, where each probe is assigned uniquely to one transcript and is excluded if it aligns to a different transcript with 24 or more perfect matches (Casneuf et al. 2007)
 
Web link http://www.bioconductor.org/packages/release/data/experiment/html/tinesath1cdf.html
Submission date Apr 17, 2009
Last update date Jan 18, 2013
Contact name Nathalie Gonzalez
E-mail(s) [email protected]
Phone +32 (0)9 331 39 56
Organization name VIB
Department Plant System Biology
Lab System Biology of Yield
Street address Technologiepark 927
City Gent
ZIP/Postal code 9052
Country Belgium
 
Samples (93) GSM393521, GSM393522, GSM393523, GSM393524, GSM393525, GSM393526 
Series (9)
GSE15722 Chromosomal duplication in the grandifolia-D mutants of Arabidopsis thaliana, expression data
GSE15726 Chromosomal duplication in the grandifolia-D mutants of Arabidopsis thaliana
GSE16474 Responses of Arabidopsis leaves to prolonged osmotic stress are mediated by their developmental stage
Relations
Alternative to GPL198 (Alternative CDF [official])

Data table header descriptions
ID
ORF Entrez Gene Link
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".
SPOT_ID

Data table
ID ORF 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 SPOT_ID
AT1G01010 At1g01010 NAC domain protein, putative similar to NAC domain protein NAM GB: AAD17313 GI:4325282 from [Arabidopsis thaliana]; supported by cDNA: gi_16612276_gb_AF439834.1_AF439834 At1g01010 839580 NM_099983 AT1G01010 0007275 // multicellular organismal development // inferred from sequence or structural similarity /// 0045449 // regulation of transcription // inferred from electronic annotation 0003677 // DNA binding // inferred from electronic annotation /// 0003700 // transcription factor activity // inferred from sequence or structural similarity
AT1G01030 At1g01030 DNA-binding protein, putative similar to RAV1 GB:BAA34250 GI:3868857 from [Arabidopsis thaliana] (Nucleic Acids Res. 27 (2), 470-478 (1999)) At1g01030 839321 NM_099985 AT1G01030 0006355 // regulation of transcription, DNA-dependent // inferred from electronic annotation /// 0009908 // flower development // inferred from mutant phenotype /// 0045449 // regulation of transcription // traceable author statement /// 0048366 // leaf development // inferred from mutant phenotype 0003677 // DNA binding // inferred from electronic annotation /// 0003700 // transcription factor activity // inferred from sequence or structural similarity
AT1G01040 At1g01040 CAF protein identical to RNA helicase/RNAseIII CAF protein GB:AAF03534 GI:6102610 from [Arabidopsis thaliana]; supported by cDNA: gi_11559644_gb_AF292940.1_AF292940 At1g01040 839574 NM_099986 AT1G01040 0000910 // cytokinesis // inferred from mutant phenotype /// 0006396 // RNA processing // inferred from sequence or structural similarity /// 0006396 // RNA processing // inferred from electronic annotation /// 0009616 // virus induced gene silencing // inferred from mutant phenotype /// 0009880 // embryonic pattern specification // inferred from mutant phenotype /// 0009908 // flower development // traceable author statement /// 0010098 // suspensor development // inferred from mutant phenotype /// 0010228 // vegetative to reproductive phase transition // inferred from mutant phenotype /// 0010267 // RNA interference, production of ta-siRNAs // inferred from mutant phenotype /// 0010599 // RNA interference, production of lsiRNA // inferred from mutant phenotype /// 0030422 // RNA interference, production of siRNA // inferred from mutant phenotype /// 0031047 // gene silencing by RNA // inferred from electronic annotation /// 0031053 // primary microRNA processing // traceable author statement /// 0035196 // gene silencing by miRNA, production of miRNAs // inferred from genetic interaction /// 0035279 // gene silencing by miRNA, mRNA cleavage // inferred from mutant phenotype 0005622 // intracellular // inferred from electronic annotation /// 0005634 // nucleus // inferred from direct assay /// 0005634 // nucleus // inferred from electronic annotation /// 0010445 // nuclear dicing body // inferred from direct assay 0000166 // nucleotide binding // inferred from electronic annotation /// 0003676 // nucleic acid binding // inferred from electronic annotation /// 0003723 // RNA binding // inferred from electronic annotation /// 0003725 // double-stranded RNA binding // inferred from direct assay /// 0003725 // double-stranded RNA binding // inferred from electronic annotation /// 0004386 // helicase activity // inferred from electronic annotation /// 0004518 // nuclease activity // inferred from electronic annotation /// 0004519 // endonuclease activity // inferred from electronic annotation /// 0004525 // ribonuclease III activity // inferred from sequence or structural similarity /// 0004525 // ribonuclease III activity // inferred from electronic annotation /// 0005515 // protein binding // inferred from physical interaction /// 0005524 // ATP binding // inferred from electronic annotation /// 0008026 // ATP-dependent helicase activity // inferred from sequence or structural similarity /// 0008026 // ATP-dependent helicase activity // inferred from electronic annotation /// 0016787 // hydrolase activity // inferred from electronic annotation
AT1G01050 At1g01050 soluble inorganic pyrophosphatase, putative similar to soluble inorganic pyrophosphatase GB: AAD46520 GI:5669924 from [Populus tremula x Populus tremuloides];supported by full-length cDNA: Ceres:124537. At1g01050 839579 NM_099987 AT1G01050 0006796 // phosphate metabolic process // inferred from electronic annotation /// 0008152 // metabolic process // inferred from sequence or structural similarity 0005634 // nucleus // inferred from direct assay /// 0005737 // cytoplasm // inferred from direct assay /// 0005737 // cytoplasm // inferred from electronic annotation /// 0016020 // membrane // inferred from sequence or structural similarity 0000287 // magnesium ion binding // inferred from electronic annotation /// 0004427 // inorganic diphosphatase activity // inferred from direct assay /// 0004427 // inorganic diphosphatase activity // inferred from electronic annotation
AT1G01060 At1g01060 DNA-binding protein, putative similar to DNA binding protein CCA1 from [Arabidopsis thaliana] At1g01060 839341 NM_001035847 /// NM_001083968 /// NM_099988 /// NM_179237 AT1G01060 0009651 // response to salt stress // inferred from expression pattern /// 0009723 // response to ethylene stimulus // inferred from expression pattern /// 0009733 // response to auxin stimulus // inferred from expression pattern /// 0009737 // response to abscisic acid stimulus // inferred from expression pattern /// 0009739 // response to gibberellin stimulus // inferred from expression pattern /// 0009751 // response to salicylic acid stimulus // inferred from expression pattern /// 0009753 // response to jasmonic acid stimulus // inferred from expression pattern /// 0045449 // regulation of transcription // traceable author statement /// 0046686 // response to cadmium ion // inferred from expression pattern /// 0048574 // long-day photoperiodism, flowering // inferred from genetic interaction 0005634 // nucleus // inferred from electronic annotation 0003677 // DNA binding // inferred from sequence or structural similarity /// 0003677 // DNA binding // inferred from electronic annotation /// 0003700 // transcription factor activity // inferred from sequence or structural similarity /// 0005515 // protein binding // inferred from physical interaction
AT1G01070 At1g01070 unknown protein ;supported by full-length cDNA: Ceres:20749. At1g01070 839550 NM_099989 /// NM_202005 AT1G01070 0016020 // membrane // inferred from electronic annotation
AT1G01080 At1g01080 ribonucleoprotein, putative similar to 33 KDA RIBONUCLEOPROTEIN GB:P19684 from [Nicotiana sylvestris];supported by full-length cDNA: Ceres:21739. At1g01080 839463 NM_001035848 /// NM_099990 AT1G01080 0005634 // nucleus // inferred from direct assay /// 0009507 // chloroplast // inferred from direct assay /// 0009570 // chloroplast stroma // inferred from direct assay /// 0009941 // chloroplast envelope // inferred from direct assay /// 0030529 // ribonucleoprotein complex // inferred from electronic annotation 0000166 // nucleotide binding // inferred from electronic annotation /// 0003676 // nucleic acid binding // inferred from electronic annotation /// 0003723 // RNA binding // inferred from sequence or structural similarity
AT1G01090 At1g01090 pyruvate dehydrogenase E1 alpha subunit identical to pyruvate dehydrogenase E1 alpha subunit GB:AAB86803 GI:2454182 from [Arabidopsis thaliana]; supported by cDNA: gi_15450706_gb_AY052721.1_ At1g01090 839429 NM_099991 AT1G01090 0006096 // glycolysis // inferred from electronic annotation /// 0008152 // metabolic process // inferred from sequence or structural similarity /// 0008152 // metabolic process // inferred from electronic annotation /// 0055114 // oxidation reduction // inferred from electronic annotation 0009507 // chloroplast // inferred from direct assay /// 0009536 // plastid // inferred from sequence or structural similarity /// 0009941 // chloroplast envelope // inferred from direct assay /// 0043231 // intracellular membrane-bounded organelle // inferred from electronic annotation 0004739 // pyruvate dehydrogenase (acetyl-transferring) activity // inferred from sequence or structural similarity /// 0004739 // pyruvate dehydrogenase (acetyl-transferring) activity // inferred from electronic annotation /// 0016491 // oxidoreductase activity // inferred from electronic annotation /// 0016624 // oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor // inferred from electronic annotation
AT1G01100 At1g01100 acidic ribosomal protein, putative similar to 60S ACIDIC RIBOSOMAL PROTEIN P1 GB:O23095 from [Arabidopsis thaliana];supported by full-length cDNA: Ceres:24367. At1g01100 839410 NM_001083969 /// NM_001083970 /// NM_099992 /// NM_179238 AT1G01100 0006414 // translational elongation // inferred from sequence or structural similarity /// 0006414 // translational elongation // inferred from electronic annotation 0005622 // intracellular // inferred from electronic annotation /// 0005840 // ribosome // inferred from sequence or structural similarity /// 0005840 // ribosome // inferred from electronic annotation /// 0005886 // plasma membrane // inferred from direct assay /// 0022626 // cytosolic ribosome // inferred from direct assay /// 0030529 // ribonucleoprotein complex // inferred from electronic annotation 0003735 // structural constituent of ribosome // inferred from sequence or structural similarity /// 0003735 // structural constituent of ribosome // inferred from electronic annotation
AT1G01110 At1g01110 unknown protein ;supported by full-length cDNA: Ceres:148018. At1g01110 839394 NM_001123732 /// NM_099993 AT1G01110 0005739 // mitochondrion // inferred from electronic annotation
AT1G01120 At1g01120 fatty acid elongase 3-ketoacyl-CoA synthase 1 identical to GB:AAC99312 GI:4091810 from [Arabidopsis thaliana] At1g01120 fatty acid elongase 3-ketoacyl-CoA synthase 1 (KCS1) KCS1 839395 NM_099994 AT1G01120 0000038 // very-long-chain fatty acid metabolic process // inferred from direct assay /// 0006633 // fatty acid biosynthetic process // inferred from electronic annotation /// 0008152 // metabolic process // inferred from electronic annotation /// 0009409 // response to cold // inferred from expression pattern /// 0009416 // response to light stimulus // inferred from expression pattern /// 0010025 // wax biosynthetic process // inferred from direct assay /// 0010025 // wax biosynthetic process // inferred from mutant phenotype /// 0030497 // fatty acid elongation // inferred from direct assay /// 0042335 // cuticle development // inferred from mutant phenotype 0005783 // endoplasmic reticulum // inferred from direct assay /// 0016020 // membrane // inferred from sequence or structural similarity /// 0016020 // membrane // inferred from electronic annotation /// 0016021 // integral to membrane // inferred from electronic annotation /// 0022626 // cytosolic ribosome // inferred from direct assay 0003824 // catalytic activity // inferred from electronic annotation /// 0008415 // acyltransferase activity // inferred from sequence or structural similarity /// 0008415 // acyltransferase activity // inferred from electronic annotation /// 0009922 // fatty acid elongase activity // inferred from direct assay /// 0016740 // transferase activity // inferred from electronic annotation /// 0016747 // transferase activity, transferring acyl groups other than amino-acyl groups // inferred from electronic annotation /// 0033807 // icosanoyl-CoA synthase activity // inferred from electronic annotation
AT1G01130 At1g01130 hypothetical protein contains similarity to serine threonine kinase GB:CAA73067 GI:2632252 from (Sorghum bicolor) At1g01130 839359 NM_099995 AT1G01130
AT1G01140 At1g01140 serine/threonine kinase, putative similar to serine/threonine kinase GB:CAA73067.1 GI:2632252 from [Sorghum bicolor]; supported by cDNA: gi_14423523_gb_AF386999.1_AF386999 At1g01140 839349 NM_099996 /// NM_179239 /// NM_179240 AT1G01140 0006468 // protein amino acid phosphorylation // inferred from electronic annotation /// 0007165 // signal transduction // inferred from electronic annotation 0000166 // nucleotide binding // inferred from electronic annotation /// 0004672 // protein kinase activity // inferred from electronic annotation /// 0004674 // protein serine/threonine kinase activity // inferred from electronic annotation /// 0005524 // ATP binding // inferred from electronic annotation /// 0016301 // kinase activity // inferred from sequence or structural similarity /// 0016301 // kinase activity // inferred from electronic annotation /// 0016740 // transferase activity // inferred from electronic annotation /// 0030145 // manganese ion binding // inferred from electronic annotation
AT1G01150 At1g01150 hypothetical protein predicted by genemark.hmm, contains Pfam profile:PF00249 Myb-like DNA-binding domain At1g01150 839294 NM_099997 AT1G01150 0045449 // regulation of transcription // inferred from electronic annotation 0003677 // DNA binding // inferred from electronic annotation /// 0008270 // zinc ion binding // inferred from electronic annotation
AT1G01160 At1g01160 unknown protein ; supported by cDNA: gi_15294231_gb_AF410307.1_AF410307 At1g01160 839278 NM_099998 AT1G01160 0005634 // nucleus // inferred from sequence or structural similarity 0003713 // transcription coactivator activity // inferred from sequence or structural similarity /// 0005515 // protein binding // inferred from physical interaction
AT1G01170 At1g01170 unknown protein At1g01170 839263 NM_001035849 /// NM_099999 AT1G01170 0006950 // response to stress // inferred from sequence or structural similarity 0005739 // mitochondrion // inferred from direct assay /// 0016020 // membrane // inferred from direct assay
AT1G01180 At1g01180 hypothetical protein identical to hyothetical protein GB:AAF26464 GI:6715637 from (Arabidopsis thaliana) At1g01180 839239 NM_100000 AT1G01180
AT1G01190 At1g01190 cytochrome P450, putative similar to cytochrome P450 GB:L23209 GI:349717 from (Zea mays) At1g01190 839233 NM_100001 AT1G01190 0012505 // endomembrane system // inferred from electronic annotation 0019825 // oxygen binding // inferred from sequence or structural similarity
AT1G01200 At1g01200 GTP-binding protein, putative similar to GTP-binding protein GB:D12541 GI:303735 from [Pisum sativum] At1g01200 839493 NM_100002 AT1G01200 0007264 // small GTPase mediated signal transduction // inferred from electronic annotation /// 0015031 // protein transport // inferred from electronic annotation 0005634 // nucleus // inferred from direct assay 0000166 // nucleotide binding // inferred from electronic annotation /// 0005525 // GTP binding // inferred from sequence or structural similarity /// 0005525 // GTP binding // inferred from electronic annotation
AT1G01220 At1g01220 hypothetical protein similar to unknown protein GB:AAF32477 GI:6957733 from [Arabidopsis thaliana] At1g01220 839420 NM_100004 AT1G01220 0008152 // metabolic process // inferred from electronic annotation /// 0016310 // phosphorylation // inferred from electronic annotation 0005737 // cytoplasm // inferred from electronic annotation 0004335 // galactokinase activity // inferred from sequence or structural similarity /// 0005524 // ATP binding // inferred from sequence or structural similarity

Total number of rows: 20777

Table truncated, full table size 11307 Kbytes.




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