Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae.
The mRNA and protein expression in Saccharomyces cerevisiae cultured in rich or minimal media was analyzed by oligonucleotide arrays and quantitative multidimensional protein identification technology. The overall correlation between mRNA and protein expression was weakly positive with a Spearman rank correlation coefficient of 0.45 for 678 loci. To place the data sets in a proper biological context, a clustering approach based on protein pathways and protein complexes was implemented. Protein expression levels were transcriptionally controlled for not only single loci but for entire protein pathways (e.g., Met, Arg, and Leu biosynthetic pathways). In contrast, the protein expression of loci in several protein complexes (e.g., SPT, COPI, and ribosome) was posttranscriptionally controlled. The coupling of the methods described provided insight into the biology of S. cerevisiae and a clustering strategy by which future studies should be based.
Washburn
Michael P
MP
Proteomics, Torrey Mesa Research Institute, 3115 Merryfield Row, San Diego, CA 92121, USA. michael.washburn@syngenta.com
Koller
Antonius
A
Oshiro
Guy
G
Ulaszek
Ryan R
RR
Plouffe
David
D
Deciu
Cosmin
C
Winzeler
Elizabeth
E
Yates
John R
JR
D000595:Amino Acid Sequence; D016000:Cluster Analysis; D003627:Data Interpretation, Statistical; D020869:Gene Expression Profiling / Q000706:statistics & numerical data; D005800:Genes, Fungal; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data; D010455:Peptides / Q000235:genetics / Q000378:metabolism; D040081:Protein Array Analysis / Q000706:statistics & numerical data; D012331:RNA, Fungal / Q000235:genetics* / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism*
D010455:Peptides; D012331:RNA, Fungal; D012333:RNA, Messenger; D029701:Saccharomyces cerevisiae Proteins