The following steps were taken to define the EcoToxModule gene sets:
- Choosing biological processes that are relevant to ecotoxicology (the EcoToxModules) that fall into five larger categories (the EcoToxProcesses)
- Sorting individual KEGG pathways into appropriate EcoToxModules
- Annotating transcripts from the six EcoToxChip species with KEGG IDs using the KofamScan software
- Assigning EcoToxChip genes to EcoToxModules if their transcripts were annotated with KEGG IDs that belong to the selected pathways
- Manually considering the EcoToxChip genes to add any obvious module assignments that were missing. For example, KEGG pathways for vertebrates were based off mammalian species, and so do not contain vitellogenin. We manually assigned this important toxicology biomarker to “Endocrine - Reproduction”.
For more details, please refer to this paper