Table 1 Overrepresentation of MIPS functional categories in genes that were differentially transcribed in response to fully fermentative conditions. Clusters A&B, 2 & 3 and 4, 5 & 6 had similar expression pattern and similar enrichments, and were therefore pooled before the overrepresentation analysis. Enrichment was estimated by hypergeometric distribution analysis (cut-offs around 10^-5, see Materials and Methods); magnitude of the enrichment is indicated by the p-value.

01

METABOLISM

01.01

   amino acid metabolism

01.01.06

metabolism of the aspartate family

01.01.06.05.01

biosynthesis of methionine

01.03

   nucleotide metabolism

01.03.01

purine nucleotide metabolism

01.03.01.03

purine nucleotide anabolism

01.05.01

   C-compound and carbohydrate utilization

01.05.01.07.03

tetrahydrofolate-dependent C-1-transfer

11

TRANSCRIPTION

11.02.01

   rRNA synthesis

11.02.02

   tRNA synthesis

11.04

RNA processing

11.04.01

   rRNA processing

11.06

RNA modification

11.06.01

   rRNA modification

12

PROTEIN SYNTHESIS

12.01

   ribosome biogenesis

12.01.01

ribosomal proteins

14

PROTEIN FATE (folding, modification, destination)

14.07.02

   modification with sugar residues

14.07.02.01

O-directed glycosylation

16

PROTEIN WITH BINDING FUNCTION

16.03

   nucleic acid binding

16.03.03

RNA binding

20

CELLULAR TRANSPORT, TRANSPORT FACILITATION...

20.01.13

   lipid transport

MIPS_cat.

nr.

   description

01

METABOLISM

01.05

   C-compound and carbohydrate metabolism

01.05.01.01.01

sugar, glucoside, polyol and carboxylate catabolism

01.06

   lipid, fatty acid and isoprenoid metabolism

01.06.01.07

isoprenoid metabolism

01.06.01.07.11

tetracyclic and pentacyclic triterpenes biosynthesis

02

ENERGY

02.10

   tricarboxylic-acid pathway

02.11

   electron transport & membrane-ass. energy conservation

02.13

   Respiration

02.13.03

aerobic respiration

02.19

   metabolism of energy reserves

02.25

   oxidation of fatty acids

02.45.15

energy generation (e.g. ATP synthase)

11

TRANSCRIPTION

11.02.03.04.01

   transcriptional activator

14

PROTEIN FATE (folding, modific., destination)

14.07.11

   protein processing (proteolytic)

14.13

   protein degradation

14.13.01

cytoplasmic and nuclear protein degradation

14.13.01.01

proteasomal degradation

20

CELLULAR TRANSPORT, TRANSPORT FAC.

20.01.15

electron/hydrogen transport

20.09

   transport routes

32

CELL RESCUE, DEFENSE AND VIRULENCE

32.01

   stress response

32.01.01

oxydative stress response

32.01.07

unfolded protein response (ER quality control)

42

BIOGENESIS OF CELL. COMPONENTS

42.16

   mitochondrion