Analyis of Genomes and Transcriptomes in terms of the Occurrence of Protein Parts and Features

Mark Gerstein
Molecular Biophysics & Biochemistry
Yale University
PO Box 208114
New Haven, CT 06520-8114 USA
telephone: 203 432 6105
fax: 360 838 7861
email: Mark.Gerstein@yale.edu
prestype: Platform
presenter: Mark Gerstein

Mark Gerstein, Ronald Jansen, Amar Drawid, Dov Greenbaum
Molecular Biophysics & Biochemistry Department, Yale University, New Haven, CT 06520

SUMMARY

My talk will focus on analyzing genomes and gene-expression data in terms of the finite list of protein "parts". Depending on context, a part could be a structural fold or sequence superfamily. I will touch on the following topics:

* How one can compare different genomes in terms occurrence of various parts in them. And how this idea can be extended to compare the representation of parts in the genome versus the transcriptome. In particular, this allows one to see what protein features are enriched in highly expressed proteins.

* How one can analyze the relationship between where a part is located and its transcriptome occurrence -- i.e. between a protein's subcellular localization and its level of gene expression. We extend this work to develope a formal Bayesian system for predicting subcellular localization, partially based on gene expression data.

* To what degree is protein function and protein-protein interactions related to similarities in the level of gene expression. Based on developing a statistical significance formalism, I will argue that while there is a definite relationship for certain classes of protein functions and protein-protein interactions, the relationship is not general and global. The absence of correlation is principally due to the inconsistent way protein function is defined.

REFERENCES



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