Protein feature based identification of cell cycle regulated proteins in yeast.
DNA microarrays have been used extensively to identify cell cycle regulated genes in yeast; however, the overlap in the genes identified is surprisingly small. We show that certain protein features can be used to distinguish cell cycle regulated genes from other genes with high confidence (features include protein phosphorylation, glycosylation, subcellular location and instability/degradation). We demonstrate that co-expressed, periodic genes encode proteins which share combinations of features, and provide an overview of the proteome dynamics during the cycle. A large set of novel putative cell cycle regulated proteins were identified, many of which have no known function.
de Lichtenberg
Ulrik
U
Center for Biological Sequence Analysis, BioCentrum, The Technical University of Denmark, Building 208, DK-2800, Lyngby, Denmark.
Jensen
Thomas S
TS
Jensen
Lars J
LJ
Brunak
Søren
S
D002453:Cell Cycle / Q000235:genetics*; D018797:Cell Cycle Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D002455:Cell Division / Q000235:genetics; D004261:DNA Replication / Q000235:genetics; D004271:DNA, Fungal / Q000235:genetics / Q000378:metabolism; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism*; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D008938:Mitosis / Q000502:physiology*; D016571:Neural Networks, Computer; D020411:Oligonucleotide Array Sequence Analysis; D010766:Phosphorylation; D020543:Proteome; D012331:RNA, Fungal / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D014158:Transcription, Genetic
D018797:Cell Cycle Proteins; D004271:DNA, Fungal; D005656:Fungal Proteins; D020543:Proteome; D012331:RNA, Fungal