Differentially Expressed Gene (DEG) Selection

We calculated the expression levels as fragments per kilobase of transcript per million mapped reads (FPKM) for each sample. The DEGs were identified in female or male floral buds at three different differentiation stages using DESeq to detect the differentially expressed genes. Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.10.1). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.01 & FC (Fold Change) ≥3 found by DESeq were assigned as differentially expressed. All of the DEGs were used for the COG, GO, KEGG, KOG, Pfam, Swiss-Prot, eggNOG and Nr functional annotation analyses.