Use in Hypothesis Generation and Testing
Sometimes, a scientist already has an idea what is going on, a hypothesis, and he or she performs an expression profiling experiment with the idea of potentially disproving this hypothesis. In other words, the scientist is making a specific prediction about levels of expression that could turn out to be false.
More commonly, expression profiling takes place before enough is known about how genes interact with experimental conditions for a testable hypothesis to exist. With no hypothesis, there is nothing to disprove, but expression profiling can help to identify a candidate hypothesis for future experiments. Most early expression profiling experiments, and many current ones, have this form which is known as class discovery. A popular approach to class discovery involves grouping similar genes or samples together using k-means or hierarchical clustering. The figure above represents the output of a two dimensional cluster, in which similar samples (rows, above) and similar gene probes (columns) were organized so that they would lie close together. The simplest form of class discovery would be to list all the genes that changed by more than a certain amount between two experimental conditions.
Class prediction is more difficult than class discovery, but it allows one to answer questions of direct clinical significance such as, given this profile, what is the probability that this patient will respond to this drug? This requires many examples of profiles that responded and did not respond, as well as cross-validation techniques to discriminate between them.
Read more about this topic: Gene Expression Profiling
Famous quotes containing the words hypothesis, generation and/or testing:
“The wheels and springs of man are all set to the hypothesis of the permanence of nature. We are not built like a ship to be tossed, but like a house to stand.”
—Ralph Waldo Emerson (18031882)
“The greater part of our best years has been passed for our generation in these two great worldconvulsions. All will be changed after this war, which spends in one month more than nations earned before in years ... there is no more security in our time than in those of the Reformation or the fall of Rome.”
—Stefan Zweig (18811942)
“Traditional scientific method has always been at the very best 20-20 hindsight. Its good for seeing where youve been. Its good for testing the truth of what you think you know, but it cant tell you where you ought to go.”
—Robert M. Pirsig (b. 1928)