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Table 1 Temperature and hypoxia treatment effects on the extracted scores of the first two principal components

From: The transcriptomic responses of Atlantic salmon (Salmo salar) to high temperature stress alone, and in combination with moderate hypoxia

Linear Mixed-Effect Models For Each Principal Component (PC-1 and PC-2)a

Microarrayb

PC

Var %

Factors

Num DF

Den DF

F-value

p-value

CT vs WN

CT vs WH

WN vs WH

All Probes (17,072)

PC-1

16.6

Intercept

1

12

20.6

7e-4

   

Treatment

2

3

384.6

2e-4

2e-4

0.001

0.489

PC-2

10.4

Intercept

1

12

0.4

0.531

   

Treatment

2

3

1.0

0.477

   

DEPs WN & WH (1111)

PC-1

61.5

Intercept

1

12

19.1

9e-4

   

Treatment

2

3

687.6

1e-4

< 0.0001

2e-4

0.841

PC-2

4.6

Intercept

1

12

0.3

0.623

   

Treatment

2

3

1.0

0.470

   

DEPs WN (789)

PC-1

46.6

Intercept

1

12

819.3

< 0.0001

   

Treatment

2

3

506.0

2e-4

6e-4

2e-4

0.012

PC-2

6.3

Intercept

1

12

1.8

0.209

   

Treatment

2

3

0.9

0.506

   

DEPs WH (994)

PC-1

42.1

Intercept

1

12

252.3

< 0.0001

   

Treatment

2

3

875.0

1e-4

0.002

< 0.0001

0.007

PC-2

7.7

Intercept

1

12

0.6

0.441

   

Treatment

2

3

0.0

0.982

   

qPCRc

          

All Target Genes (41)

PC-1

39.4

Intercept

1

18

147.5

< 0.0001

   

Treatment

2

3

318.4

3e-4

3e-4

6e-4

0.747

PC-2

18.2

Intercept

1

18

46.9

< 0.0001

   

Treatment

2

3

1.2

0.416

   

Stress-Related Genes (24)

PC-1

45.9

Intercept

1

18

713.9

< 0.0001

   

Treatment

2

3

488.3

2e-4

1e-4

2e-4

0.537

PC-2

19.6

Intercept

1

18

16.9

7e-4

   

Treatment

2

3

1.2

0.423

   

Immune-Related Genes (14)

PC-1

30.7

Intercept

1

18

1.5

0.237

   

Treatment

2

3

32.8

0.009

0.011

0.012

0.405

PC-2

23.6

Intercept

1

18

0.0

0.870

   

Treatment

2

3

1.2

0.417

   
  1. a Linear mixed-effect models (LMEs) were performed for the first two principal components (PC-1 and PC-2) individually to assess the effect of the fixed factor ‘treatment’ and included the random term ‘tank’. The variance explained by each PC is indicated in percentage (%) values. For the pairwise comparisons between the Control (CT), Warm & Normoxic (WN) and Warm & Hypoxic (WH) treatment groups, lsmeans post-hoc tests with Tukey’s multiple comparisons adjustment of p-values were applied. Significant p-values are marked in bold letters (p < 0.05)
  2. b Statistical approach based on normalized log2 ratios of 17,072 detected microarray probes, 1111 WN & WH-specific differentially expressed probes (DEPs), 789 WN-specific DEPs and 994 WH-specific DEPs
  3. c Statistical approach based on the relative expression values (RQ) of 41 target genes, 24 stress-related genes and 14 immune-related genes measured with qPCR (Fluidigm Biomarkâ„¢) (see Table 2)
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BMC Genomics

ISSN: 1471-2164

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