Expression-based discovery of candidate ovule development regulators through transcriptional profiling of ovule mutants

Additional file 1:

Scatterplots comparing methods of normalization and expression summarization. A pair of hybridization replicates, ant 1 E and ant 2 E, were chosen to illustrate differences in data distribution after processing with different methods to produce a final expression measure for each gene. All values are log₂ transformed and ant 1E gene values are plotted on the y-axis against ant 2 E on the x-axis. The red line indicates no difference in expression level between replicates, and the black lines indicate 2-fold changes between the replicates. Larger numbers of points far from the red diagonal indicate less correspondence between the replicates. Results were similar for a separate set of replicates (not shown). (A) RMA; (B) dchip perfect match (PM) only; (C) MAS 5.0; (D) dchip perfect match minus mismatch (PM-MM).

Format: TIFF Size: 8MB Download file

Additional file 2:

Pearson correlation coefficients between replicates, comparing different processing methods. Comparisons for all replicates between processing with RMA, dchip perfect match (PM) only, dchip perfect match minus mismatch (PM-MM), and MAS 5.0. Higher values indicated better correlation between replicates.

Format: PDF Size: 57KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 3:

Overlap between genes identified as significantly changed between mutant and wildtype using dchip and RMA-limma. (A) WT E vs ant E; (B) WT F vs ino F.

Format: PDF Size: 69KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 4:

Fold change values for genes known to be expressed in ovules as determined with two different analysis methods. Fold changes are WT/mutant, with numbers > 1 indicating a decrease in the mutant. NI indicates those genes that were not selected by the test indicated.

Format: PDF Size: 138KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 5:

SOM clusters for 800 genes significantly decreased in ant E arrays compared with both WT E and inoE. Clustering using SOM principles with an input of 12 clusters leads to the groups shown. The number of genes contained within each cluster is indicated in each box. The z-transformed (mean = 0; standard deviation = 1) gene expression values form the y-axis of each graph. Each black dot represents the mean expression level of all the genes in the cluster for an array. The order of the arrays is EARLY arrays first, with three WT followed by three ino and three ant. The FULL arrays are next (two WT followed by two ino) and the WT LATE arrays are listed last. The red lines show the upper and lower ranges of the expression values for the genes within the cluster.

Format: JPEG Size: 303KB Download file

Additional file 6:

Selected genes with known carpel expression patterns identified by the arrays. Genes are grouped by the similarity of their expression profiles in the arrays, and the published expression pattern in pistils is described.

Format: PDF Size: 166KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 7:

Genes predicted to be expressed in the inner integument, ovule primordia and/or medial regions. Listed genes showed good evidence of expression in the indicated ovule regions on the basis of being either 2-fold decreased in the relevant mutant or showing a significant decrease in more than one mutant:wild type comparison. The fold changes between the pair-wise comparisons are given (natural scale) and a negative value indicates that the mutant value was less than the wild-type value. Genes are organized by broad functional categories, and for inner integument genes the cluster to which they were assigned is noted. For outer integument genes, the evidence of expression was from the EARLY or FULL arrays as noted. The * column shows whether a gene was putatively absent in any mutant and whether a gene was also identified in the analyses by Yu [33], Johnston [34] and Tung [31]. (a: mutant level less than 3.58 (log₂); es: embryo sac; tt: transmitting tract; s: stigma).

Format: XLS Size: 48KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 8:

Genes predicted to be expressed in the outer integument. As for additional file 7

Format: XLS Size: 34KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 9:

Genes predicted to be expressed in both integuments. As for additional file 7

Format: XLS Size: 24KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional file 10:

Mean natural scale RMA values of putatively root specific genes in the 17 pistil arrays. Table of genes used to estimate expression value for genes expected to be absent in the samples used.

Format: PDF Size: 33KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 11:

Genes tested with qRT-PCR and primers used. Table of genes validated with qRT-PCR.

Format: PDF Size: 56KB Download file

This file can be viewed with: Adobe Acrobat Reader