生物信息学讲课预案.ppt

Periodicity of 32 Alu Sequences 谢谢各位！ * Conceptually, each “ome” map can be conceived as a two-dimensional matrix. The X axis represents the genome, the complete set of ORFs (ORFeome; see Walhout et al., 2000b), or the proteome. The Y axis repre-sents a set of conditions, genetic back-grounds or phenotypes, or even the proteome itself (see text for details). Overlapping maps in the Z axis constitute the biological atlas. * Hypothesis-driven research concentrates on one protein and uses many different tools for its characterization. We refer to the vertical arrow as the “vertical approach.” Large-scale functional genomics experiments apply the same tool to many if not all genes or proteins. We refer to the horizontal arrow as the “horizontal approach.” * New, better algorithms Integration. Collaboration Complex queries, e.g. “what are the known protein kinases in the yeast genome that are involved in cell division and how many of these have homologues in plants?” * c, A portion of the molecular interaction map for the regulatory network that controls the mammalian cell cycle 6 . Colours indicate different types of interactions: black, binding interactions and stoichiometric conversions; red, covalent modifications and gene expression; green, enzyme actions; blue, stimulations and inhibitions. * Strategies used to link functionally related yeast proteins, showing the number of links provided by each method. 4,130 very high confidence links were constructed from experimental data, between proteins of related metabolic function, and from links generated by at least two of the prediction methods. 19,521 high confidence links were constructed from the phylogenetic profile method when unconfirmed by other techniques. The remaining links were considered to be of lower confidence. Links associate proteins of related function and can therefore be used to predict the function of many uncharacterized proteins. The phylogenetic profile method 1 identifies functionally related pr