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Figure 2 | BMC Genomics

Figure 2

From: Global analysis of gene expression in NGF-deprived sympathetic neurons identifies molecular pathways associated with cell death

Figure 2

Schematic overview of gene-level analysis. Rat sympathetic neurons were cultured in vitro for 6 days and then maintained in 1) medium containing NGF, or 2) medium without NGF supplemented with anti-NGF antibody or 3) medium without NGF containing anti-NGF antibody and the MLK inhibitor CEP-11004 at 400 nM. Three independent experiments were performed. After 16 hours, RNA was isolated and processed and gene expression analysed using Affymetrix rat exon microarrays. The summarisation algorithm, PLIER (Probe Logarithmic Intensity Error) was used to compute gene-level expression values. At the gene level, we identified 1228 differentially expressed genes with a Limma FDR (false discovery rate) adjusted p-value of < 0.05. This number of differentially expressed genes was reduced to 48 up-regulated and 86 down-regulated genes when applying a more stringent statistical test (FDR adjusted p-value < 0.01) and an absolute fold change threshold of > 2. A - see additional file 1 for a list of these genes. B - see additional file 2 for a list of these genes.

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