geneXplain’s Upstream Analysis
What is Upstream Analysis?
GeneXplain’s proprietary approach to analyze gene expression data is called Upstream Analysis. The term indicates that it is a causal analysis, providing a clue about the reason why a certain set of genes has been up- (or down-) regulated in the system under study. In contrast, conventional analyses usually reveal the effects of the differentially expressed genes, e.g. by mapping them onto ontological categories.
How does it work?
- At first, the promoters of the differentially regulated genes are retrieved and analyzed for potential transcription factor (TF) binding sites and their combinations. From that, a set of TFs is identified that potentially have regulated the found DEGs.
- In a second step, the pathways are reconstructed that are known to activate the previously hypothesized TFs. Molecules where these pathways converge are considered as potential master regulators of the process under study
Step 1: Promoter analysis
Next, out of all these potential transcription factor binding sites (TFBSs), those that are characteristic for the DEG set under study are identified. This is done by rigorously determining their enrichment in the Yes- compared to the No set.
Learn more about promoter analysis with TRANSFAC® in the geneXplain platform.
Step 2: Pathway analysis
Activities of transcription factors (TFs, blue circles) are regulated by upstream signaling cascades (components shown as green circles). These converge in certain nodes, representing molecules that are potential master regulators of the process under study.