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

Mark Gerstein
Molecular Biophysics & Biochemistry Department
Yale University
New Haven, CT 06520

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

http://bioinfo.mbb.yale.edu

M Gerstein & R Jansen (2000). "The current excitement in
bioinformatics, analysis of whole-genome expression data: How does it
relate to protein structure and function?"
Curr. Opin. Struc. Biol. (in press).

A Drawid, R Jansen & M Gerstein (2000). "Gene Expression Levels are
Correlated with Protein Subcellular Localization," Trends in Genetics
16: 426-430.

A Drawid & M Gerstein (2000). "A Bayesian System Integrating
Expression Data with Sequence Patterns for Localizing Proteins:
Comprehensive Application to the Yeast Genome,"
J. Mol. Biol. 301:1059-75

R Jansen & M Gerstein (2000). "Analysis of the Yeast Transcriptome
with Broad Structural and Functional Categories: Characterizing Highly
Expressed Proteins," Nuc. Acids Res. 28:1481-1488

M Gerstein (1998). "Patterns of Protein-Fold Usage in Eight Microbial
Genomes: A Comprehensive Structural Census," Proteins 33: 518-534.