Integrative Genomics: Surveys of a Finite Parts List

Mark Gerstein

P Harrison, J Qian, V Alexandrov, P Bertone, R Das, D Greenbaum, R
Jansen, W Krebs N Echols, J Lin, C Wilson, A Drawid, N Lan, B Stenger

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

http://bioinfo.mbb.yale.edu

My talk will focus on analyzing genomes and functional genomics data
in terms of the finite list of protein "parts". I use the term "part"
rather broadly, and depending on context, it can either be a protein
fold or family. I will touch on SOME of the following topics: (i) How
one can compare different genomes in terms of the occurrence of
parts. (ii) How one can do the exact same operation on the
pseudogenome -- the total complement on pseudogenes in an organism.
(iii) How this idea can be further extended to analyze gene expression
datasets. With regard expression data, I compare analyses in terms of
various proteomic categories -- e.g. families, functions,
interactions, and localization.

References

Qian J, Stenger B, Wilson CA, Lin J, Jansen R, Teichmann SA, Park J,
      Krebs WG, Yu H, Alexandrov V, Echols N, Gerstein M (2001).
      "PartsList: a web-based system for dynamically ranking protein
      folds based on disparate attributes, including whole-genome
      expression and interaction information."  Nucleic Acids
      Res. 29:1750-64.

      www.partslist.org 

P Harrison , N Echols , M Gerstein (2001). "Digging for Dead Genes: An
      Analysis of the Characteristics of the Pseudogene Population in
      the C. elegans Genome." Nuc. Acids. Res. 29: 818-830.

A Drawid , R Jansen , M Gerstein (2000). "Genome-wide analysis
      relating expression level with protein subcellular
      localization." Trends Genet 16 : 426-30 .

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 .

J Lin , M Gerstein (2000). "Whole-genome trees based on the occurrence
      of folds and orthologs: implications for comparing genomes on
      different levels." Genome Res 10 : 808-18 .

R Jansen , M Gerstein (2000). "Analysis of the yeast transcriptome
      with structural and functional categories: characterizing highly
      expressed proteins." Nucleic Acids Res 28 : 1481-8 .

M Gerstein (1998). "Patterns of protein-fold usage in eight microbial
      genomes: a comprehensive structural census." Proteins 33 :
      518-34 .