title: Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models.
abstract: BACKGROUND
  Modern transcriptomics and proteomics enable us to survey the expression of RNAs and proteins at large scales. While these data are usually generated and analyzed separately, there is an increasing interest in comparing and co-analyzing transcriptome and proteome expression data. A major open question is whether transcriptome and proteome expression is linked and how it is coordinated.
  
  
  RESULTS
  Here we have developed a probabilistic clustering model that permits analysis of the links between transcriptomic and proteomic profiles in a sensible and flexible manner. Our coupled mixture model defines a prior probability distribution over the component to which a protein profile should be assigned conditioned on which component the associated mRNA profile belongs to. We apply this approach to a large dataset of quantitative transcriptomic and proteomic expression data obtained from a human breast epithelial cell line (HMEC). The results reveal a complex relationship between transcriptome and proteome with most mRNA clusters linked to at least two protein clusters, and vice versa. A more detailed analysis incorporating information on gene function from the Gene Ontology database shows that a high correlation of mRNA and protein expression is limited to the components of some molecular machines, such as the ribosome, cell adhesion complexes and the TCP-1 chaperonin involved in protein folding.
  
  
  BACKGROUND
  Matlab code is available from the authors on request.
authors.affiliation: Department of Computing Science, University of Glasgow, Glasgow G128QQ, UK. srogers@dcs.gla.ac.uk
authors.forename: Simon
authors.initials: S
authors.lastname: Rogers
authors.forename: Mark
authors.initials: M
authors.lastname: Girolami
authors.forename: Walter
authors.initials: W
authors.lastname: Kolch
authors.forename: Katrina M
authors.initials: KM
authors.lastname: Waters
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.forename: Brian
authors.initials: B
authors.lastname: Thrall
authors.forename: H Steven
authors.initials: HS
authors.lastname: Wiley
mesh_terms: D016000:Cluster Analysis; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D011506:Proteins / Q000737:chemistry; D020543:Proteome / Q000032:analysis / Q000378:metabolism*; D040901:Proteomics / Q000379:methods; D012333:RNA, Messenger / Q000378:metabolism
chemical_list: D011506:Proteins; D020543:Proteome; D012333:RNA, Messenger