ORA was conducted using Qiagen’s Ingenuity Pathway Analysis (IPA) tool (Qiagen, USA) on differentially expressed genes with p < 0.01 and absolute fold-change ≥ 1.5-fold, for each tissue. Statistical significance of over-represented pathways was ascertained via Fisher's exact test and adjusted for multiple testing via the FDR according to Benjamin-Hochberg [8 ].
Pathway Enrichment Analysis of Transcriptomics Data
ORA was conducted using Qiagen’s Ingenuity Pathway Analysis (IPA) tool (Qiagen, USA) on differentially expressed genes with p < 0.01 and absolute fold-change ≥ 1.5-fold, for each tissue. Statistical significance of over-represented pathways was ascertained via Fisher's exact test and adjusted for multiple testing via the FDR according to Benjamin-Hochberg [8 ].
Corresponding Organization : Pennington Biomedical Research Center
Other organizations : Duke-NUS Medical School, Georgia State University
Variable analysis
- DESeq2 normalized expression signals
- Enrichment of a priori defined biological pathways from the KEGG repository
- Over-represented pathways from Ingenuity Pathway Analysis (IPA)
- Size-matched random gene-sets used for permutation testing to determine statistical significance of pathway enrichment
- Not explicitly mentioned
- Not explicitly mentioned
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