Summary of cBR Expression Patterns.

<p>Note: The cut-off value for the Up, Down and No change of cBR expression in early and late germination phase is 1.4-fold change.</p

Biological Pathways and Protein Families Over- and Under-Represented with Early and Late Germination Regulated cBRs.

<p>Figure 3A showed biological pathways and families over- and under-represented with early or late germination regulated cBRs. The functionalities were displayed on the right; and the germination phase and regulation patterns were displayed on the top. The representation analysis was conducted for all cBRs. Log2 fold change values in early and late germination phases were used in the PageMan analysis. Fisher's exact test and an ORA Cutoff value of 1 were used. A false color scale was used to indicate the statistic Z value. Blue and red indicates significance in over-representation and under-representation. The cBRs encoding proteins in cell wall metabolism and peroxidase families were preferentially regulated in early germination phase (Figure 3B and 3C) while the cBRs encoding proteins in chromatin structure/modeling pathways were preferentially up-regulated in late germination phase (Figure 3D). Log2 of average fold changes from dry seed over the course of germination for the cBRs in those pathways were graphed. Dry, middle (Mid) and end (End) points of germination were indicated as X-axis.</p

Relationship Between Protein Sequence Similarity and Expression Similarity of Barley and Rice Genes.

<p>Relationship Between Protein Sequence Similarity and Expression Similarity of Barley and Rice Genes.</p

Distribution of cBRs and Their Expression Patterns in Biological Pathways.

<p>All cBRs were assigned to 35 functional categories defined by MapMan tools. The log2 of average fold changes from dry seed over the course of germination for each cBR were graphed next to its functional categories. The number of cBRs assigned to each functional group was listed in the table.</p

The cBRs and Their Expression Patterns and Functions.

<p>The cBRs and Their Expression Patterns and Functions.</p

Biological Pathways and Protein Families Composed of cBRs with Divergent Expression Patterns.

<p>The cBRs encoding G-proteins and 14-3-3 proteins (4A), proteins in ubiquitin dependent degradation pathways (4B), cysteine and serine proteases (4C), and alpha and beta amylases (4D) with diverse expression patterns were shown. Log2 of average fold changes in reference to dry seeds over the course of germination for each cBR was graphed. Dry, middle (Mid) and end (End) points of germination were indicated X-axis. The diagram of ubiquitin dependent degradation pathway was displayed in 4B.</p

Summary of Germination Regulated BRs and cBRs.

<p>Summary of Germination Regulated BRs and cBRs.</p

Distribution of Pearson Correlation Co-efficiency between Expression Patterns of Barley and Rice Genes.

<p>The germination regulated barley and rice genes (BRs) were paired randomly and paired based on their sequence similarity with an e-value less than −50 respectively; and their PCC values were determined. The distribution of PCC value for BR genes with e-value less than −50 (dark blue) were compared with randomly paired BR genes (light blue). The percentage of BRs (Y-axis) in each defined PCC value range (X-axis) was graphed.</p

Interactions of miR395, 319 and 159 with Their Target Genes.

<p>Interactions of miR395, 319 and 159 (red circles) with their target genes (light blue circles and pink circles) are shown. Two targets are commonly regulated by miR319 and miR395 while seven targets are commonly regulated by miR319 and miR159.</p

Sequence Alignment of Inverted Repeats and a Neutral Invertase Gene.

<p>The central regions of the inverted repeat sequences 1 to 8, their homologous IR sequences from chromosomes 8, 2, 14 and 20 and a fragment of a neutral invertase gene (Glyma12g02690) were aligned. The miRNA and miRNA star sequences are highlighted in green and blue, respectively. Nucleotides that differ from the consensus sequence are shaded in red.</p