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Table 1 Gene Ontology categories over-represented in some comparisons between variables

From: Common gene expression strategies revealed by genome-wide analysis in yeast

 

Rates

Amounts

 

GO*

P

a-P

No. of genes§

GO

P

a-P

No. of genes

High correlation

        

   Both low level (4-5)

Cell cycle

<E-17

<0.001

159/370

Cell cycle

<E-7

0.001

112/300

 

Meiosis

<E -6

0.003

52/122

-

   
 

Regulation of physiological process

<E-16

<0.001

204/518

Regulation of physiological process

<E-10

<0.001

171/459

 

DNA binding

<E -12

<0.001

88/190

DNA binding

<E -8

<0.001

66/146

 

Protein kinase activity

<E -13

<0.001

64/117

-

   
 

DNA metabolism

<E -11

<0.001

158/422

DNA metabolism

<E -5

0.017

39/372

 

Response to endogenous stimulus

<E -6

0.004

65/164

-

   
 

Regulation of transcription

<E -10

<0.001

120/298

Regulation of transcription

<E -6

0.001

99/263

 

-

   

RNA splicing

<E -6

0.002

47/103

 

Lipid kinase activity

<E -5

0.005

8/8

-

   

   Both high level (1-2)

Cytosolic ribosome

<E -24

<0.001

93/147

Cytosolic ribosome

<E -78

<0.001

149/156

 

Protein biosynthesis

<E -15

<0.001

179/439

Protein biosynthesis

<E -48

<0.001

247/417

 

Hydrogen ion transporter activity

<E -6

0.001

25/43

Hydrogen ion transporter activity

<E -11

<0.001

33/43

 

-

   

Carboxylic acid metabolism

<E -18

<0.001

134/258

 

Mitochondrial matrix

<E -7

0.001

64/150

-

   
 

Redox activity

<E -8

<0.001

93/228

Redox activity

<E -17

<0.001

107/197

 

Mitochondrial ribosome

<E -5

0.01

36/78

-

   
 

-

   

Ribosome biogenesis

<E -14

<0.001

97/182

 

Proteasome complex

<E -8

<0.001

28/43

Proteasome complex

<E -13

<0.001

36/45

 

Nucleotide metabolism

<E -5

0.044

35/79

Nucleotide metabolism

<E -11

<0.001

49/79

 

Endoplasmic reticulum

<E -7

0.001

127/356

Endoplasmic reticulum

<E -07

<0.001

118/290

 

Hexose catabolism

<E -5

0.007

17/26

Hexose catabolism

<E -06

0.005

18/26

 

Protein folding

<E -6

0.001

33/62

-

   
 

-

   

Cell wall

<E -6

0.001

29/50

Low correlation

        

   Low level in RNA (4/5), high in protein (1/2)

Ribosome biogenesis

<E -5

0.022

24/190

    
 

Spore wall assembly

<E -6

0.006

10/35

    
 

Glycoprotein biosynthesis

<E -5

0.01

13/66

    
 

Oxidoreductase activity, acting on the CH-CH group

<E -5

0.019

5/9

    
 

Protein amino acid glycosylation

<E -5

0.046

12/62

    

   Low level in protein (4/5), high in RNA (1/2)

-

   

Membrane

< E -6

0.001

46/665

 

-

   

Transporter activity

< E -6

0.001

24/246

 

-

   

Cell wall

< E -6

0.002

10/50

 

-

   

Vacuole

< E -5

0.012

15/128

  1. *Comparisons were done as in Figure 2. Then, the genes corresponding to different levels of correlation were divided into groups according to their expression level and the GOs were searched. Only statistically significant categories are shown. High correlation class includes both very high and high correlation classes from Figure 2b, while the low correlations include both low and very low correlations classes, also from Figure 2b. Absolute p value. Adjusted p value. §The number of genes shows how many of the genes in the GO category present among the genes analyzed in each pairwise comparison are within the selected quintile.