Background: The last two decades have seen several new methods for analysing gene expression data. One such method is pathway analysis in which it’s possible to decipher response patterns between pathways (groups of interacting genes) and external stress factors. A critical issue in pathway analysis is often limited sample sizes resulting in undesirable batch affects. A method for reducing such effects, called Centralization Within Sub-Experiments (CSE), has recently been developed. This method makes it possible to predict pathways using data from experiments with a diversity of external conditions. Aims: We propose a method for identifying stress-responsive pathways predicted using CSE pre-processed expression data. Method: 27 CSE predicted pathways were analysed and tested for stress-responsiveness associated with specific external stress factors. Firstly, we screened the complete gene list for DE genes. Secondly, we analysed the occurrences of DE genes within each pathway and finally, an over-representation analysis was performed with the aim of identifying pathways with significantly larger portions of differently expressed genes categorised as stress-responsive. Results: The analysis resulted in a list of pathways with significantly larger proportions of DE genes. This was only when screened for salt-responsive pathways. We also found that these pathways contained several mitochondrial genes confirmed to be associated with salt stress. Conclusion: The results show great promise in using the method for extracting information regarding the stress responsiveness amongst pathways predicted using CSE-pre-processing expression data.
| Identifer | oai:union.ndltd.org:UPSALLA1/oai:DiVA.org:umu-177326 |
| Date | January 2020 |
| Creators | Lindqvist, Anton |
| Publisher | Umeå universitet, Institutionen för fysik |
| Source Sets | DiVA Archive at Upsalla University |
| Language | English |
| Detected Language | English |
| Type | Student thesis, info:eu-repo/semantics/bachelorThesis, text |
| Format | application/pdf |
| Rights | info:eu-repo/semantics/openAccess |
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