The 530 genes with an average Cy5/Cy3 ratio greater than 2.0 were used for the highly expressed dataset while the 527 genes with an average Cy5/Cy3 ratio less than 1.15 were used for the least expressed dataset.
Ingenuity Pathways Analysis (IPA) of statistically differentially expressed dataset containing 25 unique STBM proteins identified the significant biological functions and pathways.
Statistically differentially expressed dataset containing 25 unique proteins and their corresponding IPI identifier, p-value and fold change values were uploaded into the IPA.
In every instance this simple shuffling of the data completely abrogated detection of the enrichment signal, supporting the SBSE score as a robust estimate of seed enrichment in a differentially expressed dataset.
Statistically differentially expressed dataset containing 1159 genes and their corresponding probesets ID, Gene symbol, Entrez gene ID as clone identifier, p-value and fold change values were uploaded into the IPA.
Gene ontology terms associated with mitochondrial functions (oxidation biological processes, monooxygenase and catalytic molecular functions, and iron, heme, and tetrapyyrole binding) were enriched in the significantly differentially expressed dataset.
Together, the consistency in functionalities of the highly expressed dataset in all three arthropods studied herein reveals that optimization of codon and amino acid usage is a shared feature of highly expressed genes, particularly those involved in cell division and translation, in these divergent arthropods.
The correlation values presented with stably expressed dataset (Group 1) are the highest reported up to the present date, and they indicate that selection for gene sequence characteristics towards expression efficiency in human genes may be more relevant than previously believed.
A norsolorinic acid reductase homologue (MGG_01713.6; induced in rice, barley, PQ, and MM-C) and two other putative aflatoxin precursor homologues were also present in our differentially expressed dataset, which are a sterigmatocystin 8-O-methyltransferase precursor (MGG_02120.6; induced in rice, barley, PQ, and MM-N) and a versicolorin reductase (MGG_07216.6; induced in all treatments except PQ).
The differentially expressed datasets was also subjected to Ingenuity pathway analysis (www.ingenuity.com).com
