Using RNA transcriptional data and Ingenuity IPA^®,
de-regulated molecular pathways were identified
in each of the experimental groups.

RNA-seq

Transcriptional analysis (RNA-seq) was completed using the tool DESeq, with gene expression approximated by Reads Per Kilobase per Million (RPKM). Individual genes were analyzed for significant de-regulation with reference to control liver, with p-values adjusted for a false discovery rate of 5%.

Genes which were significantly de-regulated with reference to control liver were sent to IPA for pathway analysis. Samples with a large number of significantly de-regulated genes were not able to have all of their genes included in the pathway analysis.

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Pathway identification

Ingenuity Pathway Analysis (IPA) provides detailed analyses on which pathways are most significantly de-regulated in a comparison between two transcriptional profiles, by utilizing its extensive evidence-based repository of gene information. For each comparison with control liver, significantly involved pathways are identified with the following information:

P-value: Overall pathway significance, corrected for false discovery
Z-score: Predicted activation (positive) or inhibition (negative) of the pathway, available only for pathways with sufficient literature evidence.
Ratio: Ratio of genes in the pathway which are significantly de-regulated relative to the control group.

Grouping pathways

IPA results may include information on up to 600 pathways, which can make pathway interpretation appear daunting. In order to provide an overview of which types of pathways are involved in each experimental group, pathways were grouped into 13 larger categories using IPA’s internal category scheme. Details on how specific categories were assembled can be found when viewing a pathway within Navigator.