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Pipeline publication

[…] o FDR cutoff was used for the ethanol contrasts in the KO mice due to less robust effects. For these comparisons, the top 25 genes were shown based on uncorrected nominal significance. False discovery rate (FDR) adjustment for multiple testing was performed on the main and interaction effects, with a cutoff of 0.3 or less used for single gene findings. Post-hoc contrasts were obtained using a Fisher's Protected Least Significant Difference, without correction for multiple testing. Functional enrichment analysis of the 50 most-robustly affected genes for each contrast of interest was performed based on the Gene Ontology (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes) annotation using Partek Pathway. We also transferred the normalized data from Partek Flow into Partek Genomics Suite to perform Pathway ANOVA using the KEGG annotation database. This procedure tests for shifts in the expression of all of the transcripts represented in a particular gene set, rather than annotating the most robustly-changed in a particular contrast., Laser dissected RNA samples of discrete lamina in the somatosensory cortex (layers 2–3 combined, layer 4, layer 5, layer 6) and discrete regions of the hippocampus (CA1 and dentate gyrus) were obtained using the previously described staining methods, with the exception that the dissected cells were collected into RLT Lysis Buffer from the RNeasy Kit (Qiagen, Valencia, CA). These RNA samples (6 per group for each region of i […]

Pipeline specifications

Software tools Partek Pathway, Partek Flow, Partek Genomics Suite
Databases KEGG Annotation
Organisms Mus musculus
Diseases Mitochondrial Diseases, Fetal Diseases, Alcohol-Related Disorders, Fetal Alcohol Spectrum Disorders
Chemicals Ethanol