Identification of expressed genes was based on FPKM and RPGM values being higher than the minimum estimates from Fig. f: Venn diagram comparing genes considered as expressed in Bm PGs on V-0 or V-6 of the 5th instar. Circles indicate the gene with the least RPGM and FPKM value that was identified as expressed by qPCR (see text for details). Dashed lines indicate the coordinates above which all genes are considered as expressed.

For each gene, the RPGM values derived from Bowtie2 versus the transcript levels (yellow circles), determined by qPCR, and FPKM values derived from Cufflinks versus the transcript levels (green circles), determined by qPCR, are plotted. e: Identification of the critical RPGM and FPKM value above which all genes are considered as expressed on V-6 of the 5th instar. d: Determination of the critical RPGM and FPKM value above which all genes are considered as expressed on V-0 of the 5th instar. Dashed arrows define the coordinates above which all genes are considered as expressed (see text for details). For each gene, the RPGM (Reads Per Gene Model) derived from Bowtie2 were plotted against the FPKM (Fragments Per Kilobase of transcript per Million of mapped reads) derived from Cufflinks. c: Correlation between the Bowtie2 and Cufflinks results output on V-6 of the 5th instar. b: Correlation between the Bowtie2 and Cufflinks results output on V-0 of the 5th instar.

a: Schematic workflow that identified genes differentially (Diff.) and/or highly expressed in the Bm PGs on V-0 and V-6 of the 5th instar. Quantitative and qualitative parameters of gene expression in Bombyx mori prothoracic glands.

Cufflinks hidata