Fig. 6

Functional enrichment of genes prioritized by SIFT score or phylogenetic nucleotide conservation (PNC), in maize. Genes were prioritized by selecting SNPs with SIFT conservation (1 − SIFT score) or predicted PNC above the 50%, 90%, 99%, or 99.9% percentile, or observed PNC equal to 1 (tree size > 5, substitution rate < 0.05). A Difference in average expression between prioritized genes and all genes. Gene expression is quantified by RNA abundance (FPKM over 23 tissues) and protein abundance (dNSAF over 32 tissues) based on the gene expression atlas of [29]: median expression, and number of tissues with non-zero expression level. Error bars and dotted lines represent 95% confidence intervals in two-sample t-tests, for predicted and observed PNC, respectively. B Enrichment of prioritized genes for gene ontology (GO) classes. Ratio of number of prioritized genes over expected number under the null hypothesis (random gene prioritization). GO classes belong to the plant GO slim subset [30]. Ontology: BP, biological process; MF: molecular function. For each threshold and ontology, false discovery rates (FDR) were calculated over GO classes, based on P-values from Fisher’s exact tests. Full circles and full lines indicate FDR < 0.05, for SIFT conservation or predicted PNC, and observed PNC, respectively