Table 1 Significant over-representation of GO categories (BP and MF) among genes, which showed different transcription levels between all genes expressed on the microarray and the different experimental groups

From: Transcriptome-wide signature of hybrid breakdown associated with intrinsic reproductive isolation in lake whitefish species pairs (Coregonus spp. Salmonidae)

Comparison

Category

Description a

Fold b

Count (%)c

P-value d

Number of GO terms a

Backcross-moribund/backcross-healthy

BP

Generation of precursor metabolites and energy

1.74

67 (10.2%)

0.000

1

 

BP

Translational elongation

1.91

28 (4.2%)

0.066

1

 

MF

Structural molecule activity

1.49

65 (9.8%)

0.022

1

 

MF

Hydrogen ion transporter activity

1.86

28 (4.2%)

0.047

1

Backcross-moribund/dwarf

BP

Generation of precursor metabolites and energy

1.72

60 (10.1%)

0.000

1

 

BP

Translation

1.84

70 (11.7%)

0.022

2

 

MF

Structural molecule activity

1.58

62 (10.4%)

0.006

1

Backcross-moribund/normal

BP

Generation of precursor metabolites and energy

1.78

63 (10.3%)

0.000

1

 

BP

Translational elongation

2.07

28 (4.6%)

0.010

1

 

MF

Cytoskeletal protein binding

1.75

38 (6.2%)

0.021

1

Backcross-healthy/dwarf

BP

Glycolysis

21.08

6 (22.2%)

0.001

1

 

BP

Alcohol catabolic process

15.17

6 (22.2%)

0.009

1

 

BP

Carbohydrate catabolic process

14.59

6 (22.2%)

0.006

4

Backcross-healthy/normal

 

—

    

Dwarf/normal

 

—

    

All genes differentially expressed and backcross-moribund overexpressed genes

BP

Generation of precursor metabolites and energy

2.09

62 (18.5%)

0.00

1

 

BP

Oxidation reduction

1.76

50 (14.9%)

0.00

1

 

BP

Electron transport chain

2.12

30 (8.9%)

0.00

1

 

BP

Phosphorylation

1.82

29 (8.6%)

0.05

1

 

MF

Catalytic activity

1.24

148 (44%)

0.00

 
 

MF

Magnesium ion binding

2.05

21 (6.3%)

0.01

 
 

MF

Ion transporter activity

1.80

28 (8.2%)

0.02

9

All genes differentially expressed and

BP

Translation

1.41

69 (15.4%)

0.001

1

backcross-moribund underexpressed genes

BP

Gene expression

1.29

136 (30.3%)

0.000

1

 

BP

Macromolecule metabolic process

1.26

182 (40.4%)

0.00

4

 

BP

RNA metabolic process

1.45

48 (10.7%)

0.033

2

 

MF

Structural constituent of ribosome

1.48

8.9 (40%)

0.029

1

 

MF

Nucleic acid binding

1.32

86 (19.2%)

0.016

2

All genes differentially expressed and

BP

Translation

3.91

22 (48.9%)

0.000

1

essential genes differentially expressed

BP

Gene expression

2.64

32 (71.1%)

0.000

1

 

BP

Macromolecule biosynthetic process

2.08

30 (66.7%)

0.002

6

 

BP

Protein metabolic process

1.97

32 (71.9%)

0.001

3

 

MF

Structural constituent of ribosome

5.20

16 (35.6%)

0.000

1

 

MF

Structural molecule activity

3.25

16 (35.6%)

0.002

1

  1. Abbreviations: BP, biological process; GO, gene ontology; MF, molecular function.
  2. aSimilar GO terms were grouped together as one category using the most inclusive GO term provided (for example, macromolecule metabolic process grouped within macromolecule biosynthetic process). Number of original GO terms in each category was written in number of GO terms column.
  3. bFold enrichment values given by DAVID as compared to the background group (either genes expressed or all genes differentially expressed).
  4. cNumber of unigenes in GO category and percentage of total.
  5. dNote that when more than one GO term were included in the same category, the P-value (Ease score (Bonferroni correction implemented by Huang et al., 2009)) was the mean P-values of all the GO terms.
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