Supplemental Data

Files in this Data Supplement:

• Supplemental Figure 1 - Results of experiments with the flower-specific cDNA array. Expression profiles of ap1-1 (A), ap2-2 (B), ap3-3 (C), pi-1 (D), and ag-3 (E) inflorescences were compared to that of wild-type inflorescences. Plots were generated from experimental data of four replicates with biologically independent samples after normalization and replicate analysis (see Methods for details). M = log₂ (I_MT/I_WT); A = 0.5 log₂ (I_MT·I_WT), where I_MT and I_WT are signal intensities for a given element in a mutant or wild type, respectively.
• Supplemental Figure 2 - Self-organizing map generated from elements of the flower-specific cDNA array that showed significant expression changes in at least one of the experiments. Elements that are upregulated in wild type compared with the mutant are colored in yellow, downregulated elements in blue. The intensities of the colors increase with the increasing expression differences as indicated on the left. The diagram was generated with the programs Cluster and Treeview (Eisen et al., 1998) using log₂ transformed expression ratios. The clusters predicted to contain organ-specific transcripts are indicated. Ca, carpel; St, stamen; Pe, petal.
• Supplemental File 1 - Protocols used for the microarray experiments.
• Supplemental File 2 - Information about the array contruction processes, promoter analyses, and access to microarray data.
• Supplemental Table 1 - A list of all organ-expressed genes described in the study. Gene identifiers, gene names, gene symbols, gene aliases, and the predicted organ of expression are indicated.
• Supplemental Table 2 - Genes among the organ-expressed genes encoding putative transcription factors are listed. In the worksheet Transcription Factors, the predicted organ of expression and the transcription factor family are indicated for each gene. In the worksheet Families, the frequency of members of different transcription factor families among the organ-expressed genes are shown.
• Supplemental Table 3 - Genes among the organ-expressed genes with predicted expression in pollen are listed. In the two left-most columns, data from a previous study by Honys and Twell (2003) are shown. Genes predicted to be specifically expressed in pollen are highlighted in yellow. Genes that were found in the previous study and that are also present in the data set of organ-expressed genes are indicated (column “In data set?”).
• Supplemental Table 4 - Results of the analysis of gene ontology annotations for the organ-expressed genes are shown for the organizing principle “component.” In the worksheet Annotations, all available gene ontology annotations for the organ-expressed genes are shown. In the worksheet Distribution, the frequencies of terms within the genome-wide data set and the organ-expressed genes are given (columns “Genome” and “Organs”). To detect enrichment or under-representation of a given term among the organ-expressed genes, the ratio between the percentage distribution of this term in the reported data set and in the genome was calculated. For the 50 most frequent terms in the genome, comparisons are listed in the worksheet TOP 50.
• Supplemental Table 5 - Results of the analysis of gene ontology annotations for the organ-expressed genes are shown for the organizing principle “function.” In the worksheet Annotations, all available gene ontology annotations for the organ-expressed genes are shown. In the worksheet Distribution, the frequencies of terms within the genome-wide data set and the organ-expressed genes are given (columns “Genome” and “Organs”). To detect enrichment or under-representation of a given term among the organ-expressed genes, the ratio between the percentage distribution of this term in the reported data set and in the genome was calculated. For the 100 most frequent terms in the genome, comparisons are listed in the worksheet TOP 100.
• Supplemental Table 6 - Results of the analysis of gene ontology annotations for the organ-expressed genes are shown for the organizing principle “process.” In the worksheet Annotations, all available gene ontology annotations for the organ-expressed genes are shown. In the worksheet Distribution, the frequencies of terms within the genome-wide data set and the organ-expressed genes are given (columns “Genome” and “Organs”). To detect enrichment or under-representation of a given term among the organ-expressed genes, the ratio between the percentage distribution of this term in the reported data set and in the genome was calculated. For the 100 most frequent terms in the genome, comparisons are listed in the worksheet TOP 100.
• Supplemental Table 7 - The organ-expressed genes identified with the flower-specific cDNA array and with the oligonucleotide array are listed (worksheets cDNA and Operon, respectively). In the worksheets cDNA vs Operon, the data obtained with the flower-specific cDNA array were compared with the organ-expressed genes identified with the oligonucleotide array.
• Supplemental Table 8 - Information about gene families in the Arabidopsis genome was obtained from TAIR (http://www.arabidopsis.org/info/genefamily/genefamily.html). The distribution of gene families among the organ-expressed genes was determined and compared with the genome-wide distribution. In the worksheet Annotations, available gene family annotations for the organ-expressed genes are shown. In the worksheet Distribution, the frequencies of families within the genome-wide data set and the organ-expressed genes are given (columns “Genome” and “Organs,” respectively).
• Supplemental Table 9 - Related proteins encoded by the organ-expressed genes were identified as described in Results. The pairs found in the stamen and carpel groups are listed. In the first four columns, gene identifiers and names of the query sequences followed by bit scores and E-values of self-to-self comparisons are shown. The genes related to the query are listed with the corresponding bit scores and E-values.
• Supplemental Table 10 - The presence of CArG-boxes and putative AG binding sites in the Arabidopsis genome was determined using Pattern Match (http://www.arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl). The presence of CArG-boxes (worksheet CArG Distribution) and putative AG binding sites (worksheet AG Distribution) in different regions (as described in Results) of the organ-expressed genes is indicated.
• Supplemental Table 11 - The predictions of array elements of the flower-specific cDNA array representing floral organ-expressed transcripts are summarized. The worksheet Training Set contains the values for elements representing known carpel-expressed genes that were used to enhance the prediction of carpel-specific transcripts (as described in Results). Mean log₂ transformed intensity ratios, standard deviations, and cut-off values are shown. The worksheet Carpel 2 contains the elements of the carpel group after application of the cut-off values.
• Supplemental Table 12 - The predictions of array elements of the oligonucleotide array representing floral organ-expressed transcripts are summarized. The worksheet Training Set contains the values for known carpel-expressed genes that were used to enhance the prediction of carpel-specific transcripts (as described in Results). Mean log₂ transformed intensity ratios, standard deviations, and cut-off values are shown. The worksheet Carpel 2 contains the elements of the carpel group after application of the cut-off values.
• Supplemental Table 13 - The probes and primers used for the generation of the cDNA array are listed. The worksheet Subtraction Control contains the sequences of primers used for the control of the subtraction process during the preparation of the libraries. In the worksheet Prescreening Probes all elements are listed that were used for the prescreening of the subtraction libraries. Sequences of primers used for prescreening by PCR are given in the sheet Prescreening Primers. Different colors stand for different cDNA fragments that represent a single gene and the primers that were designed to detect these fragments. The accession numbers that were initially used to identify redundant clones and the approximate position of the fragments on BAC clones are shown as well. The worksheet Vector Primers contains the sequences of primers used for the amplification of cDNA fragments. The worksheet In Situ Primers contains the sequences of primers used for the amplification of cDNA fragments used as probes for in situ hybridization.