All of the analyses described here are carried out using a set of
79-element gene expression vectors for 2467 genes in the budding yeast
S. cerevisiae [Eisen et al., 1998]. The data were collected at
various time points during the diauxic shift [DeRisi et al., 1997], the
mitotic cell division cycle [Spellman et al., 1998a],
sporulation[Chu et al., 1998], and temperature and reducing
shocks. This data was used by Eisen et al. and is available on
the Stanford web site (http://rana.stanford.edu/clustering).
Table 1: Functional classes learned by the classifiers.
Class definitions are taken from MYGD. The tricarboxylic-acid
pathway is also known as the Krebs cycle. Genes in this pathway
encode enzymes that break down pyruvate (produced from glucose) by
oxidation. This is a key catabolic pathway to produce energy for the
cell in the form of NADH and is also important for producing
intermediates in the biosynthesis of amino acids and other compounds.
The respiration chain complexes perform oxidation-reduction
reactions that capture the energy present in NADH through electron
transport and the chemiosmotic synthesis of ATP. These include the
NADH deydrogenase complex, cytochrome b-c complex, and cytochrome
oxidase complex, all embedded in the mitochondrial membrane. The
cytoplasmic ribosomal proteins are a class of proteins required to
make the ribosome, an RNA-protein complex in the cytoplasm encoded by
mRNA. This category does not include genes for the mitochondrial
ribosome. The proteasome consists of proteins comprising a
complex responsible for general degradation of proteins and other
specific protein processing events. The proteasome uses
ubiquitin, a small peptide that marks a protein to be degraded.
Histones interact with the DNA backbone to form nucleosomes which,
with other proteins, form the chromatin of the cell. Finally, the
helix-turn-helix class consists of genes that code for proteins that
contain the helix-turn-helix structural motif. This does not
constitute a functional class, and is included only as a control.
