Large-scale automated analysis of location patterns in randomly tagged 3T3 cells

Elvira García Osuna, Juchang Hua, Nicholas W. Bateman, Ting Zhao, Peter B. Berget, Robert F. Murphy*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

28 Scopus citations


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 35 clusters among the first 188 clones we obtained. This approach represents a powerful automated solution to the problem of identifying subcellular locations on a proteome-wide basis for many different cell types.

Original languageEnglish
Pages (from-to)1081-1087
Number of pages7
JournalAnnals of Biomedical Engineering
Issue number6
StatePublished - Jun 2007
Externally publishedYes


  • CD-tagging
  • Cluster analysis
  • Fluorescence microscopy
  • Location proteomics
  • Protein subcellular location
  • Subcellular location features
  • Subcellular location trees


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