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| Seminar Schedule (Seminar Organizer: Prof. Ziv Bar-Joseph) | |
Machine Learning Lunchtime Chats
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Spring 2007 Seminar
Date: April 10, 2007 Time: 09:00 AM - 10:00 AM Location: 1507 Newell-Simon Hall Speaker: Juchang Hua Biological Sciences PhD Student, ML MS Student Title: Large-Scale Automated Analysis of Protein Subcellular Location Patterns in Randomly-Tagged 3T3 Cells Abstract: Location proteomics is concerned with the systematic analysis of the subcellular location of proteins. In order to perform high-resolution, high-throughput analysis of all protein location patterns, automated methods are needed. Here we describe the use of such methods on a large collection of images obtained by automated microscopy to perform high-throughput analysis of endogenous proteins randomly-tagged with a fluorescent protein in NIH 3T3 cells. Cluster analysis was performed to identify the statistically significant location patterns in these images. This allowed us to assign a location pattern to each tagged protein without specifying what patterns are possible. To choose the best feature set for this clustering, we have used a novel method that determines which features do not artificially discriminate between control wells on different plates and uses Stepwise Discriminant Analysis (SDA) to determine which features do discriminate as much as possible among the randomly-tagged wells. Combining this feature set with consensus clustering methods resulted in 53 clusters among a dataset of 225 clones. This approach represents a powerful automated solution to the problem of identifying subcellular locations on a proteome-wide basis for many different cell types.