Figure 1.
Figure 1.

Correlation matrix of 13 maize ribonucleic acid sequencing (RNA-seq) libraries. Normalized transcript abundances for 39,456 genes in the version 2 (v2) annotation were calculated in units of fragments per kilobase pair of exon model per million fragments mapped (FPKM) with Cufflinks version 0.9.3 (Trapnell et al., 2010). Pearson product-moment correlations of log2 FPKM values were performed for all versus all tissue samples using SAS (SAS Institute, 2003). The heat map of Pearson correlation coefficents was clustered by hierarchical clustering with a Pearson correlation distance metric and average linkage using Multiple Experiment Viewer Software version 4.5 (Saeed et al., 2003). The bootstrap support values shown on tree nodes denote the percentage of times a given node was supported over 1000 resampling trials. DAP, days after pollination; Pre-em, preemergence; Post-em, postemergence.

 


Figure 2.
Figure 2.

Comparison of ribonucleic acid sequencing (RNA-seq) and microarray expression patterns. Microarray expression profiles were obtained from a previous maize atlas experiment (Sekhon et al., 2011). Log2 transformed expression values of 17,573 maize genes without predicted isoforms and present in both the RNA-seq (log2 fragments per kilobase pair of exon model per million fragments mapped [FPKM]) and microarray (log2 intensity) platforms are shown as scatter plots. Spearman correlation coefficients (SCCs) for the comparisons were determined using SAS (SAS Institute, 2003). DAP, days after pollination.

 


Figure 3.
Figure 3.

Distribution and expression of maize genes in paralogous families. Using the OrthoMCL algorithm (Li et al., 2003), ∼85% (33,457) of genes in the version 2 (v2) annotation were assigned to 4975 paralogous gene families of two or more members. A. Histogram shows the distribution of 4975 gene families. B. All maize genes are shown relative to their gene family assignment and qualitative presence or absence expression level. Genes with low confidence fragments per kilobase pair of exon model per million fragments mapped (FPKM) values equal to zero (defined by Cufflinks [Trapnell et al., 2010]) were defined as not expressed. C. Pairwise correlations of log2 FPKM expression values for genes within the same gene family were calculated, and Pearson correlation coefficients (PCCs) are summarized by gene family size. Distributions are shown compared to a set of random correlations. D. An example of gene family expression patterns is shown for a 15-member family of genes annotated as rapid alkalinization factors (RALFs). DAP, days after pollination; Pre-em, preemergence; Post-em, postemergence.

 


Figure 4.
Figure 4.

Visualization of ribonucleic acid sequencing (RNA-seq) short read mapping relative to maize gene models. Wiggle tracks indicating chromosomal positions of mapped reads were generated using the wiggles program within TopHat version 1.2.0 (Trapnell et al., 2009) and visualized with the Integrated Genome Browser (Nicol et al., 2009). The maize gene track represents genes in the version 2 (v2) annotation. Figure panels show selected genes with A. differential expression, B. female exclusive expression, C. male exclusive expression, and D. seed exclusive expression. The y axes indicate number of reads mapped. Numbers to the right of the wiggle tracks represent the normalized fragments per kilobase pair of exon model per million fragments mapped (FPKM) expression values for each tissue calculated by Cufflinks (Trapnell et al., 2010). ATPase, adenosine triphosphatase; DAP, days after pollination; Pre-em, preemergence; Post-em, postemergence.

 


Figure 5.
Figure 5.

Heat map of the eigengenes representing each gene module. The columns in the heat map represent tissue samples, and the rows represent eigengenes for each of the 17 identified coexpression modules (Langfelder and Horvath, 2007). The numbers of genes in each module are given in parentheses. The cells in the heat map show eigengene values between 0 and 1, which are indicators of relative expression levels of all genes in the module (see Materials and Methods). The labels to the right of the module numbers indicate the larger tissue subgroups where module genes show elevated expression. DAP, days after pollination; Pre-em, preemergence; Post-em, postemergence.