![]() Be able to look up and investigate KeGG maps (e.g.Metabolites, KeGG and COG over-representation Note: Confidence level will be specified in the exam set (e.g. Bonferroni adjustment of p-value threshold (How many tests were performed? -> adjust threshold).Note: Calculation p-values by hand using Fisher's Exact test will not be part of the spring 2013 exam. Automated over representation analysis:.Understand how Gene Ontology is used as labels describing function of genes/proteins (e.g.how to derive information using the "IS A" or "PART OF" relationship Understand the graphical structure of Gene Ontology.Map gene expression data to PPI networks.Perform "sanity-check" on data by plotting case v.Calculate Fold Change and Log2 transform data.Using the Network Analyzer tool in Cytoscape.Longest-shortest-path (network diameter).Random, Scale-free and Hierarchical networks.Spoke and matrix model for interpretation of protein-protein interactions (PPIs).Note: you're expected to be able to derive the pair-wise interactions from the experimental data (as we did in the exercises) and make a SIF file containing these for import into Cytoscape. Scoring of interactions - using the two methods (one for Y2H and one for Complex pulldown) we have learned in the week 2 handouts ( PDF).Attribute tables (Excel sheets or text based) - import headers ("gene name", "in input set" etc) as descriptors for the data. ![]() Note: you are expected to know how to handle (and potentially make from scratch) the different file types we have been working with:
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