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Platform GPL888 Query DataSets for GPL888
Status Public on Jan 02, 2004
Title Agilent-011839 Arabidopsis 2 Oligo Microarray G4136A (Feature Number version)
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Arabidopsis thaliana
Manufacturer Agilent Technologies
Manufacture protocol see manufacturer's web site at http://www.agilent.com/
Catalog number G4136A
 
Description
Replaced by 013324, G4136B. The content on this microarray is derived from the ATH1 v. 3 database of The Institute for Genomic Research (TIGR) and represents 21,500 genes. This microarray will be useful for scientists studying gene activity associated with various plant organ functions, stages of growth, and biotic and abiotic stresses.

Arrays of this design have barcodes that begin with 16011839 or 2511839.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL7265.
 
Submission date Jan 02, 2004
Last update date Dec 06, 2012
Organization Agilent Technologies
E-mail(s) [email protected]
Phone 877-424-4536
URL http://www.agilent.com
Department
Street address
City Palo Alto
State/province CA
ZIP/Postal code 94304
Country USA
 
Samples (129) GSM76021, GSM76022, GSM87735, GSM88340, GSM112793, GSM112794 
Series (13)
GSE3363 NST1 over-expression vs wild type
GSE3862 Low level of pathogenesis-related protein1 mRNA expression in 15-day-old Arabidopsis cer6-2 and cer2 eceriferum mutants.
GSE5043 Arabidopsis CAF-1 depletion / gamma-irradiation
Relations
Alternative to GPL7265

Data table header descriptions
ID Agilent feature number
COL Column
ROW Row
NAME Name
SPOT_ID Spot identifier
CONTROL_TYPE Control type
REFSEQ RefSeqAccession
GB_ACC GenBankAccession
UNIGENE_ID UnigeneID
TIGR_ID TIGRID
ACCESSION_STRING Accession String
CHROMOSOMAL_LOCATION Chromosomal Location
DESCRIPTION Description
GO_ID GoIDs

Data table
ID COL ROW NAME SPOT_ID CONTROL_TYPE REFSEQ GB_ACC UNIGENE_ID TIGR_ID ACCESSION_STRING CHROMOSOMAL_LOCATION DESCRIPTION GO_ID
1 105 215 BrightCorner BrightCorner pos
2 105 214 NegativeControl NegativeControl neg
3 105 213 At5g58970.1 A_84_P13137 FALSE NM_203233 AK176868 At.21660 TC264719 tair|At5g58970.1|tair|At5g58970.2|ref|NM_203233|ref|NM_125287 chr5:23826098-23826039 uncoupling protein (UCP2) identical to uncoupling protein GI:4063007 from [Arabidopsis thaliana] [At5g58970.1] GO:0006839(mitochondrial transport)|GO:0005488(binding)|GO:0006810(transport)|GO:0005743(mitochondrial inner membrane)
4 105 212 At2g03530.1 A_84_P11669 FALSE NM_126403 NM_126403 At.41387 TC268252 tair|At2g03530.1|ref|NM_126403|tc|TC268252 chr2:1073447-1073506 F-box family protein-related similar to A3 protein (Swiss-Prot:Q41706)(unknown function) [Vigna unguiculata]; contains 9 transmembrane domains; supported by tandem duplication of F-box family protein (GI:3805763) (TIGR_Ath1:At2g07140) [Arabidopsis... GO:0005739(mitochondrion)|GO:0006810(transport)|GO:0008565(protein transporter activity)|GO:0015628(type II protein secretion system)|GO:0016021(integral to membrane)|GO:0003824(catalytic activity)|GO:0004930(G-protein coupled receptor activity)|GO:0005215(transporter activity)|GO:0009252(peptidoglycan biosynthesis)|GO:0009274(cell wall (sensu Bacteria))|GO:0015627(type II protein secretion system complex)|GO:0016020(membrane)
5 105 211 At5g65060.1 A_84_P23567 FALSE NM_125905 AY231448 At.21040 TC274059 tair|At5g65060.1|ref|NM_125905|tc|TC274059|tc|TC274057 chr5:26007522-26007869 MADS-box protein (MAF3) contains Pfam profile PF00319: SRF-type transcription factor (DNA-binding and dimerisation domain); contains Pfam profile PF01486: K-box region [At5g65060.1] GO:0010048(vernalization response)|GO:0005634(nucleus)|GO:0006355(regulation of transcription, DNA-dependent)|GO:0009910(negative regulation of flower development)|GO:0003700(transcription factor activity)
6 105 210 At5g18650.1 A_84_P15865 FALSE NM_121870 NM_121870 At.20087 TC271463 tair|At5g18650.1|ref|NM_121870|tc|TC271463|gb|CA781795 chr5:6220260-6220319 zinc finger (C3HC4-type RING finger) family protein contains Pfam domain PF00097: Zinc finger, C3HC4 type (RING finger) [At5g18650.1] GO:0006355(regulation of transcription, DNA-dependent)|GO:0008270(zinc ion binding)|GO:0005489(electron transporter activity)|GO:0016567(protein ubiquitination)|GO:0020037(heme binding)|GO:0004842(ubiquitin-protein ligase activity)|GO:0005515(protein binding)|GO:0046872(metal ion binding)|GO:0000151(ubiquitin ligase complex)|GO:0003677(DNA binding)|GO:0006118(electron transport)
7 105 209 Pro25G Pro25G pos
8 105 208 At1g24130.1 A_84_P15151 FALSE NM_102259 TC278633 tair|At1g24130.1|ref|NM_102259|tc|TC278633 chr1:8534283-8534224 transducin family protein / WD-40 repeat family protein contains 7 WD-40 repeats (PF00400);similar to beta transducin-like protein HET-D2Y (GI:17225210) [Podospora anserina]. [At1g24130.1] GO:0005834(heterotrimeric G-protein complex)|GO:0000166(nucleotide binding)|GO:0009507(chloroplast)
9 105 207 At5g44240.1 A_84_P14028 FALSE NM_123791 NM_123791 At.24522 TC253582 tair|At5g44240.1|ref|NM_123791|tc|TC253582|tc|TC253581 chr5:17840498-17840557 haloacid dehalogenase-like hydrolase family protein similar to Potential phospholipid-transporting ATPase (EC 3.6.3.1) from {Mus musculus} SP|P70704, {Bos taurus} SP|Q29449; contains InterPro accession IPR005834: Haloacid dehalogenase-like hydrolase... GO:0006812(cation transport)|GO:0015693(magnesium ion transport)|GO:0016020(membrane)|GO:0005576(extracellular)|GO:0006816(calcium ion transport)|GO:0015662(ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism)|GO:0015992(proton transport)|GO:0008152(metabolism)|GO:0016021(integral to membrane)
10 105 206 At3g48970.1 A_84_P11811 FALSE NM_114756 AU236674 At.35663 TC254379 tair|At3g48970.1|ref|NM_114756|tc|TC254379|gb|AU236674 chr3:18163457-18163398 copper-binding family protein similar to copper homeostasis factor gi:3168840 from Arabidopsis thaliana; contains Pfam heavy-metal-associated domain PF00403 [At3g48970.1] GO:0046872(metal ion binding)|GO:0005507(copper ion binding)|GO:0008372(cellular_component unknown)|GO:0030001(metal ion transport)|GO:0006825(copper ion transport)
11 105 205 At3g58760.1 A_84_P13744 FALSE NM_115738 AV823277 TC254844 tair|At3g58760.1|ref|NM_115738|tc|TC254844|gb|AV823277 chr3:21742651-21742710 ankyrin protein kinase, putative similar to ankyrin-kinase [Medicago truncatula] gi|18700701|gb|AAL78674 [At3g58760.1] GO:0016301(kinase activity)|GO:0004672(protein kinase activity)|GO:0005739(mitochondrion)|GO:0005524(ATP binding)|GO:0006468(protein amino acid phosphorylation)
12 105 204 At1g47810.1 A_84_P14185 FALSE NM_103677 tair|At1g47810.1|ref|NM_103677 chr1:17606910-17606969 F-box family protein contains F-box domain Pfam:PF00646 [At1g47810.1] GO:0008372(cellular_component unknown)|GO:0005554(molecular_function unknown)
13 105 203 At1g66280.1 A_84_P11390 FALSE NM_105299 AY074378 At.18035 TC272469 tair|At1g66280.1|ref|NM_105299|tc|TC272469|gb|AY074378 chr1:24710904-24710762 glycosyl hydrolase family 1 protein contains Pfam PF00232 : Glycosyl hydrolase family 1 domain; TIGRFAM TIGR01233: 6-phospho-beta-galactosidase; similar to beta-glucosidase 1 (GI:12043529) [Arabidopsis thaliana] [At1g66280.1] GO:0004860(protein kinase inhibitor activity)|GO:0009045(xylose isomerase activity)|GO:0009405(pathogenesis)|GO:0004553(hydrolase activity, hydrolyzing O-glycosyl compounds)|GO:0005576(extracellular)|GO:0005975(carbohydrate metabolism)|GO:0012505(endomembrane system)
14 105 202 Pro25G Pro25G pos
15 105 201 At4g13340.1 A_84_P255030 FALSE NM_117407 NM_117407 At.48854 TC265491 tair|At4g13340.1|ref|NM_117407|tc|TC265491|gb|AV549431 chr4:7760803-7760862 leucine-rich repeat family protein / extensin family protein similar to extensin-like protein [Lycopersicon esculentum] gi|5917664|gb|AAD55979; contains leucine-rich repeats, Pfam:PF00560; contains proline rich extensin domains, INTERPRO:IPR002965... GO:0009664(cell wall organization and biogenesis (sensu Magnoliophyta))|GO:0005199(structural constituent of cell wall)|GO:0009928(cell surface (sensu Magnoliophyta))|GO:0012505(endomembrane system)
16 105 200 At1g11400.1 A_84_P188944 FALSE NM_101013 AY084438 At.42135 TC253970 tair|At1g11400.1|ref|NM_101013|tc|TC253970|gb|AY084438 chr1:3840127-3840186 expressed protein [At1g11400.1]
17 105 199 At4g33160.1 A_84_P13876 FALSE NM_119470 NM_119470 At.43589 TC276520 tair|At4g33160.1|ref|NM_119470|tc|TC276520|tc|AA395322 chr4:15995436-15995495 F-box family protein (FBX13) contains similarity to fimbriata GI:547307 from [Antirrhinum majus] [At4g33160.1] GO:0004842(ubiquitin-protein ligase activity)|GO:0006511(ubiquitin-dependent protein catabolism)|GO:0008372(cellular_component unknown)
18 105 198 At3g15830.1 A_84_P128101 FALSE NM_112453 TC279520 tair|At3g15830.1|ref|NM_112453|tc|TC279520 chr3:5355316-5355375 phosphatidic acid phosphatase-related / PAP2-related contains Pfam profile PF01569: PAP2 superfamily [At3g15830.1] GO:0005554(molecular_function unknown)|GO:0008372(cellular_component unknown)
19 105 197 At1g01650.1 A_84_P15026 FALSE NM_100047 AA586244 NP281109 tair|At1g01650.1|ref|NM_100047|tc|NP281109|tc|TC264572 chr1:233417-233269 protease-associated (PA) domain-containing protein contains protease associated (PA) domain, Pfam:PF02225 [At1g01650.1] GO:0006508(proteolysis and peptidolysis)|GO:0008233(peptidase activity)|GO:0008717(D-alanyl-D-alanine endopeptidase activity)|GO:0016021(integral to membrane)
20 105 196 At3g52240.1 A_84_P103646 FALSE NM_115084 AK117719 At.35316 NP234892 tair|At3g52240.1|ref|NM_115084|tc|NP234892|tc|TC255757 chr3:19383950-19383891 expressed protein [At3g52240.1] GO:0005554(molecular_function unknown)|GO:0008372(cellular_component unknown)

Total number of rows: 22575

Table truncated, full table size 9149 Kbytes.






Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp

Supplementary file Size Download File type/resource
GPL888_old_annotations.txt.gz 2.5 Mb (ftp)(http) TXT

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