Fig. 1

Quantitative and qualitative parameters of gene expression in Bombyx mori prothoracic glands. 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. b: Correlation between the Bowtie2 and Cufflinks results output on V-0 of the 5th instar. 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. Dashed arrows define the coordinates above which all genes are considered as expressed (see text for details). c: Correlation between the Bowtie2 and Cufflinks results output on V-6 of the 5th instar. 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. Dashed arrows define the coordinates above which all genes are considered as expressed (see text for details). d: Determination of the critical RPGM and FPKM value above which all genes are considered as expressed on V-0 of the 5th instar. 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. Dashed lines indicate the coordinates above which all genes are considered as expressed. Circles indicate the gene with the least RPGM and FPKM value that was identified as expressed by qPCR (see text for details). e: Identification of the critical RPGM and FPKM value above which all genes are considered as expressed on V-6 of the 5th instar. 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. Dashed lines indicate the coordinates above which all genes are considered as expressed. Circles indicate the gene with the least RPGM and FPKM value that was identified as expressed by qPCR (see text for details). f: Venn diagram comparing genes considered as expressed in Bm PGs on V-0 or V-6 of the 5th instar. Identification of expressed genes was based on FPKM and RPGM values being higher than the minimum estimates from Fig. 1d and e. g: g:Cocoa [40] results showing statistically significant overrepresented (upper panel) and underrepresented (lower panel) GO terms assigned to genes expressed on V-0 or V-6 of the 5th instar. Yellow squares show biological processes and dark green squares show molecular functions. Arrows indicate the immediate hierarchical relationship of each term