Table 1

Parametric gene set enrichment analysis of GO classes and KEGG pathways

GO category

p-value

KEGG pathway

p-value


0% vs. 0.5 or 1.0%

0% vs. 0.5 or 1.0%

Sterol transport

2.83E-08

Oxidative phosphorylation

6.63E-12

Pheromone-dependent signal transduction during conjugation with cellular fusion

5.20E-06

Arginine and proline metabolism

1.59E-09

Aerobic respiration

0.0009

Glutathione metabolism

1.26E-05

Glutamate biosynthetic process

0.0015

Citrate cycle (TCA cycle)

1.74E-05

Tricarboxylic acid cycle

0.0025

MAPK signalling pathway

2.87E-05

Exocytosis

0.0065


0% vs. 2.8%

0% vs. 2.8%

Sterol transport

1.67E-07

Arginine and proline metabolism

2.50E-13

Pheromone-dependent signal transduction during conjugation with cellular fusion

8.38E-06

Citrate cycle (TCA cycle)

4.65E-07

Glutamate biosynthetic process

7.23E-05

MAPK signalling pathway

0.0002

Tricarboxylic acid cycle

0.0006

Porphyrin metabolism

0.0009

Aerobic respiration

0.0032

Sulphur metabolism

0.0039

Exocytosis

0.0056


0% vs. 20.9%

0% vs. 20.9%

Response to stress

1.54E-06

Glyoxylate and dicarboxylate metabolism

2.77E-17

Sterol transport

2.27E-05

Citrate cycle (TCA cycle)

3.16E-12

Meiosis

0.0008

Bile acid biosynthesis

3.05E-08

NADH oxidation

0.0025

Ascorbate and aldarate metabolism

5.83E-07

Sporulation

0.0063

Nucleotide sugars metabolism

3.18E-05

Sphingolipid biosynthetic process

0.0075

Propanoate metabolism

7.84E-05

Fatty acid metabolism

0.0002

Pentose phosphate pathway

0.0004


0.5% vs. 1.0%

0.5% vs. 1.0%


0.5 or 1.0% vs. 2.8%

0.5 or 1.0% vs. 2.8%

Glyoxylate and dicarboxylate metabolism

6.15E-20

Fatty acid metabolism

0.0001

Porphyrin metabolism

0.0002


0.5 or 1.0% vs. 20.9%

0.5 or 1.0% vs. 20.9%

Sporulation (sensu Fungi)

0.0015

Pheromone-dependent signal transduction during conjugation with cellular fusion

0.0027

Meiosis

0.0048


2.8% vs. 20.9%

2.8% vs. 20.9%

Response to stress

1.1E-12

Glyoxylate and dicarboxylate metabolism

3.93E-06

Sporulation (sensu Fungi)

0.0003

Phenylalanine metabolism

0.0064

Protein folding

0.0013

Amino sugars metabolism

Pheromone-dependent signal transduction during conjugation with cellular fusion

0.0017

SRP-dependent co-translational protein targeting to membrane, translocation

0.0019

Hexose transport

0.0032

Iron ion homeostasis

0.0077


Pair wise comparison of transcriptome data from cells grown in glucose-limited chemostats receiving 0, 0.5, 1.0, 2.8 or 20.9% oxygen (p-values < 0.01). For 0.5 and 1.0% oxygen, the data has been combined and the p-values are averaged p-values.

Rintala et al. BMC Genomics 2009 10:461   doi:10.1186/1471-2164-10-461

Open Data