Example Analysis
SH-SY5Y Differentiation
SH-SY5Y is a commonly used neuroblastoma cell line. With appropriate treatment, it can be induced to differentiate into a ‘more neuronal’ form. Differentiated cells look quite different, growing thin neurites out from the body of the cell.
Image is derived from Figure 4 (Pezzini et al. 2017)
The question: What pathways are involved in SH-SY5Y Differentiation?
In their paper Transcriptomic Profiling Discloses Molecular and Cellular Events Related to Neuronal Differentiation in SH-SY5Y Neuroblastoma Cells Pezzini et al induced differentiation of the SH-SY5Y Neuroblastoma cell line and measured transcriptomic changes via RNAseq (Pezzini et al. 2017). They then looked at functional enrichment of differentially expressed genes.
The data : Differentially expressed genes
The example dataset for today is the RNAseq differential expression results.
They can be accessed via this link: http://degust.erc.monash.edu/degust/compare.html?code=5b2c7805ab8f8c5f2dc8c72e61b049b0#?plot=mds
This has been reanalysed from the published raw data, via the degust tool.
Note: Other tools and approaches will have different looking results - but generally you will end up with a table of genes with some measure of statistical confidence. The methods for functional enrichment analysis should be similar.