Comparative Transcriptomic Analyses of a Vero Cell Line in Suspension versus Adherent Culture Conditions

Table 3

Correlation between analysis methods for key findings. PEA: pathway enrichment analysis; MPA: metabolic pathway analysis; GSEA: gene set enrichment analysis; NTA: network topology-based analysis.

Key finding	Analysis methods confirming finding
Lipid metabolism	(i) PEA: lipid metabolism and lipid pathways upregulated; (ii) MPA: downregulation of CPT1 and palmitate associated metabolic reactions
Response to stress	(i) PEA: response to wounding pathway upregulated; (ii) MPA: downregulation of the proline metabolic pathway and upregulation of asparagine metabolism
Low cell density	(i) PEA: adherens junction, MYC, and E2F pathways downregulated; (ii) MPA: aspartate metabolic pathway and the mitochondrial 1-carbon metabolic pathway downregulated; (iii) GSEA: MYC and E2F pathways downregulated
Long doubling time	(i) PEA: cell division and mitotic cell cycle phase transition pathways downregulated; (ii) MA: folate metabolic pathway downregulated; (iii) GSEA: G2/M checkpoint downregulated; (iv) NTA: FYN-related PPI networks downregulated
Attempt to balance long doubling time	(i) MPA: glycine, threonine, and serine pathways upregulated; (ii) NTA: RHOU- and ESR1-related PPI networks upregulated
Upregulation of cell adhesion	(i) PEA: actin filament-based process, regulation of cell adhesion, apical part of cell, plasma membrane-bounded cell projection morphogenesis, and extracellular matrix pathways upregulated; (ii) NTA: upregulation of the cell adhesion PPI network(CDH18)