Table 3

Graph-based iterative Group Analysis of gene expression during the yeast diauxic shift.

Down-regulated genes using GeneOntology-based network


anchor locus

group description

minimal p-value

E-value

N

max. rank


YHL015W

ribosomal proteins and rRNA processing

5.87E-86

<0.01

39

48

YMR217W

amino acid and nucleotide biosynthesis

3.38E-13

2.7

9

172

YDR144C

cell wall biogenesis

4.06E-08

4.5

6

242

YNL065W

membrane transporter

4.02E-05

9.3

3

141

YLR062C

bud site selection

6.41E-05

9.9

4

367

YGL225W

protein glycosylation in Golgi

1.12E-04

10.8

4

422

YPR074C

pentose phosphate pathway

1.44E-04

11.2

4

449

total genes measured in network: 4087.

Down-regulated genes using metabolic network


anchor locus

group description

minimal p-value

E-value

N

max. rank


YNL141W

nucleotide and amino acid biosynthesis, tRNA synthetases

4.67E-59

<0.01

39

45

YOR224C

RNA polymerases

2.59E-13

1.1

23

219

total genes measured in network: 744.

Up-regulated genes using GeneOntology-based network


anchor locus

group description

minimal p-value

E-value

N

max. rank


YER065C

TCA and glyoxylate cycle, respiratory chain

8.57E-77

<0.01

39

66

YKL217W

membrane transporters (sugar, amino acids)

1.76E-15

2.3

8

62

YAL017W

protein kinases

1.07E-07

4.8

6

284

YBL043W

cell wall biogenesis

3.81E-07

5.4

4

103

YGR248W

carbohydrate metabolism

5.66E-07

5.5

5

232

YEL011W

glycogen metabolism

1.01E-06

5.8

3

42

YER037W

protein phosphatases

1.07E-06

5.8

8

736

YJL137C

glycogen biosynthesis

7.46E-06

7.3

4

215

YDL085W

disulfide oxidoreductases

1.05E-05

7.6

4

234

YNL173C

mating signal transduction

1.65E-05

8.2

4

262

YNL134C

alcohol dehydrogenase

1.34E-04

11.1

3

210

YBL038W

mitochondrial large ribosomal subunit

1.99E-04

11.9

4

487

total genes measured in network: 4087.

Up-regulated genes using metabolic network


anchor locus

group description

minimal p-value

E-value

N

max. rank


YER065C

TCA and glyoxylate cycle, respiratory chain

4.96E-53

0.11

39

54

YGR088W

cytochrome c oxidase

3.09E-10

1.2

11

106

YFR015C

glycogen synthases

2.08E-04

3.6

3

45

YJR073C

methyltransferases

3.85E-04

4.0

5

156

YDR001C

trehalases

5.01E-04

4.2

3

60

YCR014C

DNA and RNA polymerases

5.44E-04

4.2

17

481

YIR038C

glyoxalases

8.64E-04

4.5

5

183

total genes measured in network: 744.


The evidence network was constructed either from GeneOntology information (nodes are connected if they share a GeneOntology annotation) or from enzyme activity information obtained from Swissprot http://www.expasy.ch webcite. In the latter case, genes are connected if their encoded proteins convert the same substrate (as product or educt, i.e. the direction of the reaction is not taken into account here). This type of network is much smaller (only 744 genes), as only genes coding for enzymes are included. All groups that are changed with a minimal p-value smaller than 1/[number of annotated genes] are shown, sorted by significance. The corresponding E-value as estimated by the analysis of 100 random permutations of the data is also shown. The employed threshold for inclusion in the table is very generous and does not guarantee that all subgraphs shown are statistically significant. The local minimum anchoring each regulated neighborhood is indicated by its genetic locus name (for overlapping neighborhoods, only the best-ranking minimum is shown). Descriptive group names were added manually. Groups that correspond to processes discussed in the original paper are highlighted in italics. It can be seen that the highest ranking group in each case is the largest and contains the central biological processes detected by DeRisi et al. (1997) and by iGA (see Table 1 and 2). N, number of genes in each subgraph.

Breitling et al. BMC Bioinformatics 2004 5:100   doi:10.1186/1471-2105-5-100

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