Bioinformatics 91.580 2003 Spring Jianping Zhou.ppt

Extraction of functional information from large-scale gene expression data Bioinformatics 91.580 2003 Spring Jianping Zhou Contents Prominence Feature Assumption Prominence Feature Methods Prominence Feature Methods (cont) Prominence Feature Steps Prominence Feature Steps (cont) Prominence Feature Steps (cont) Prominence Feature Steps (cont) Prominence Feature Result Prominence Feature Result (cont) SP( shortest-path) analysis Introduction SP( shortest-path) analysis Discovery SP( shortest-path) analysis Discovery (cont) References * A prominence feature of cell cycle-regulated genes ----- show more remarkable and active functions than others SP( shortest-path) analysis to extract functional information ----- An alternative and complementary to clustering analysis Because of their ruling features, the cell cycle-regulated genes are assumed to be more active and remarkable than others in the Yeast Saccharomyces cerevisiae genome. When performing filtering process against original dataset by some thresholds in terms of significance, if the cell cycle-regulated genes show higher survival ratio than others, we may conclude they are more active and remarkable The preprocess utility of Gepas package can be used to prepare the comparing dataset Microarray gene data are the ideal data sources 800 Spellman’s identified cell cycle-regulated genes for Yeast Saccharomyces cerevisiae are the most complete spectrum at this point Use a single sentence of Common Lisp to count the hitting genes: (length (intersection regu (plain text file content))) ?regu: the preset CL list representing the list of 800 cell cycle-regulated gene names. It is defined in CL as: (setf regu ‘(plain text of 800 cell cycle-regulated gene)) The plain text of 800 cell cycle-regulated gene can be got by copy and paste of ORF column of CellCycle98.xls ?plain text file content: Copy and paste of preprocess or clustering output plain text file inside which the ORFs corresponding to selected