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Data resource

  In the arabidopsisGFP database, 353 Affymetrix ATH1 arrays are used. The arrays cover various organs and tissues at several developmental stages (see Legend and Dataset code list for details). This database is designed for wild type plants grown under standard conditions with no treatment (mostly controls in individual experiments).  
  NASCArrays (Nottingham Arabidopsis Stock Center Transcriptomics Service) through AffyWatch Service (Craigon et al. 2004) http://www.arabidopsis.info  
  AtGenExpress (from AFGN) http://web.uni-frankfurt.de/fb15/botanik/mcb/AFGN/atgenex.htm  
  Complete list of dataset codes of GeneChips used  


  Data normalisation  
  Datasets were normalised using freely available dChip 1.3 software (http://www.dchip.org). Present or absent calls were determined using both Affymetrix empirical MAS4 and statistical MAS 5 algorithms. All arrays were normalised to the median probe intensity level (168, baseline array ATGE_96A) and normalised CEL intensities of all arrays were used for the calculation of model-based gene-expression values based on the Perfect Match-only model (Li and Wong 2001 a,b). Among replicates, an exclusive approach for the calculation of detection calls was applied. A given gene was scored as "expressed", when it gave a reliable expression signal (Detection call "P") in all replicates (2-3 replicates) or in at least three replicates out of four (4 replicates). Expression value "0" means that detection call values did not meet the above criteria.  
  Definition of gene families  
  Gene superfamilies and families were defined according to TAIR (http://www.arabidopsis.org) and references therein. Genes comprising Arabidopsis transcription factor families were derived by compilation of data available at The Ohio State University Arabidopsis Gene Regulatory Information Server (http://arabidopsis.med.ohio-state.edu), data published in databases and databases homology searches. Remaining gene families were defined according to individual publications as referred to in corresponding sections.  
  Citing arabidopsisGFP database  
  When citing arabidopsisGFP database, please refer to the http://arabidopsisGFP.ueb.cas.cz.  
  Craigon DJ, James N, Okyere J, Higgins J, Jotham J, May S (2004) NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Res 32 Database issue: D575-577
Li C, Wong WH (2001a) Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci USA 98: 31-36
Li C, Wong WH (2001b) Model-based analysis of oligonucleotide arrays: Model validation, design issues and standard error application. Genome Biol 2: research 0032.1-0032.11