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Table 3 Functional annotation analysis of time-dependent effects of resistance training

From: Increased biological relevance of transcriptome analyses in human skeletal muscle using a model-specific pipeline

Comparison

Normalization model

Gene ontology category

ID

Description

Rank P-value

Gene-set enrichment analysis (GSEA)

ORA P-value

GSEA P-value

NES

Week 2

Tissue offset

Biological process

GO:0043062

Extracellular structure organization

7.28e−41

5.92e−25

1.96

9.04e−28

GO:0006954

Inflammatory response

1.28e−30

5.92e−25

1.79

9.04e−28

GO:0002274

Myeloid leukocyte activation

4.48e−24

3.87e−14

1.59

2.40e−16

GO:0050900

Leukocyte migration

4.79e−22

4.62e−18

1.82

2.20e−17

GO:0002444

Myeloid leukocyte mediated immunity

3.46e−20

4.71e−12

1.57

8.98e−15

Cellular component

GO:0031012

Extracellular matrix

5.85e−70

5.45e−51

2.17

3.58e−52

GO:0062023

Collagen containing extracellular matrix

1.19e−68

3.15e−47

2.20

5.88e−53

GO:0005788

Endoplasmic reticulum lumen

6.10e−24

2.71e−12

1.75

5.21e−17

GO:0005581

Collagen trimer

1.29e−21

9.26e−14

2.24

1.29e−10

Molecular function

GO:0005201

Extracellular matrix structural constituent

1.70e−40

3.56e−24

2.23

8.04e−30

Effective library size

Biological process

GO:0043062

Extracellular structure organization

1.28e−34

6.94e−23

2.03

4.27e−29

GO:0006954

Inflammatory response

3.11e−26

3.15e−21

1.82

9.15e−28

GO:0050900

Leukocyte migration

5.50e−18

1.58e−13

1.83

8.59e−15

GO:0030199

Collagen fibril organization

1.01e−17

2.75e−11

2.28

2.49e−14

GO:0042330

Taxis

5.63e−17

1.74e−12

1.69

2.15e−16

Cellular component

GO:0031012

Extracellular matrix

2.64e−63

7.23e−43

2.17

1.48e−53

GO:0062023

Collagen containing extracellular matrix

2.38e−61

4.14e−38

2.20

4.43e−52

GO:0005581

Collagen trimer

3.52e−20

8.15e−12

2.23

1.18e−14

GO:0005788

Endoplasmic reticulum lumen

8.79e−18

2.51e−12

1.87

1.50e−10

Molecular function

GO:0005201

Extracellular matrix structural constituent

9.00e−38

6.36e−18

2.18

2.82e−28

Naïve

Biological process

GO:0043062

Extracellular structure organization

1.38e−40

2.25e−23

1.93

3.36e−26

GO:0006954

Inflammatory response

1.30e−31

2.61e−26

1.78

5.70e−28

GO:0002274

Myeloid leukocyte activation

3.44e−23

4.99e−14

1.57

6.42e−16

GO:0050900

Leukocyte migration

7.26e−23

8.32e−17

1.79

7.78e−20

GO:0042330

Taxis

2.04e−19

4.63e−18

1.69

5.41e−17

Cellular component

GO:0031012

Extracellular matrix

4.84e−71

2.20e−54

2.15

7.81e−53

GO:0062023

Collagen containing extracellular matrix

9.15e−70

7.75e−49

2.19

1.01e−53

GO:0005788

Endoplasmic reticulum lumen

4.50e−24

2.56e−12

1.72

4.68e−18

GO:0005581

Collagen trimer

8.56e−22

1.06e−13

2.20

2.17e−11

Molecular function

GO:0005201

Extracellular matrix structural constituent

1.98e−40

4.68e−25

2.20

6.38e−29

Week 12

Tissue offset

Biological process

GO:0043062

Extracellular structure organization

1.86e−49

2.01e−28

2.22

1.09e−37

GO:0001501

Skeletal system development

7.13e−21

6.49e−14

1.77

1.09e−16

GO:0030199

Collagen fibril organization

2.46e−20

4.83e−12

2.48

1.29e−15

Cellular component

GO:0031012

Extracellular matrix

8.63e−72

3.48e−58

2.47

2.23e−69

GO:0062023

Collagen containing extracellular matrix

4.96e−69

4.97e−54

2.52

8.25e−67

GO:0005581

Collagen trimer

3.65e−25

1.27e−19

2.64

2.40e−25

GO:0005788

Endoplasmic reticulum lumen

8.11e−20

1.85e−10

1.84

1.87e−13

Molecular function

GO:0005201

Extracellular matrix structural constituent

2.46e−47

1.34e−34

2.63

4.24e−46

GO:0005539

Glycosaminoglycan binding

1.48e−20

3.73e−15

2.15

2.01e−17

GO:0008201

Heparin binding

5.72e−19

1.03e−15

2.25

9.82e−16

Effective library size

Biological process

GO:0043062

Extracellular structure organization

1.79e−44

3.76e−21

1.90

8.48e−33

GO:0030199

Collagen fibril organization

4.77e−19

3.05e−08

2.10

2.69e−10

Cellular component

GO:0031012

Extracellular matrix

6.91e−67

6.04e−41

2.03

2.38e−61

GO:0062023

Collagen containing extracellular matrix

1.43e−63

2.57e−38

2.07

2.59e−56

GO:0005581

Collagen trimer

1.74e−24

6.46e−13

2.17

1.11e−26

GO:0005788

Endoplasmic reticulum lumen

1.45e−17

8.84e−09

1.66

1.58e−13

Molecular function

GO:0005201

Extracellular matrix structural constituent

3.54e−45

1.48e−21

2.13

4.31e−42

GO:0005198

Structural molecule activity

3.18e−20

2.05e−14

1.61

NA

GO:0005539

Glycosaminoglycan binding

1.36e−18

2.43e−12

1.90

1.05e−15

GO:0008201

Heparin binding

2.49e−18

7.91e−11

1.95

6.20e−16

Naïve

Biological process

GO:0043062

Extracellular structure organization

2.90e−52

1.61e−39

2.94

1.06e−28

GO:0001501

Skeletal system development

7.74e−23

3.14e−18

2.21

1.05e−11

GO:0030199

Collagen fibril organization

2.99e−21

1.57e−15

3.14

5.82e−08

Cellular component

GO:0031012

Extracellular matrix

1.49e−81

7.09e−79

3.31

2.66e−44

GO:0062023

Collagen containing extracellular matrix

4.03e−79

1.04e−69

3.39

4.01e−46

GO:0005581

Collagen trimer

5.29e−27

6.03e−27

3.39

4.83e−12

GO:0005788

Endoplasmic reticulum lumen

8.14e−24

5.17e−16

2.37

1.45e−14

Molecular function

GO:0005201

Extracellular matrix structural constituent

1.22e−50

7.93e−48

3.59

6.42e−28

GO:0005539

Glycosaminoglycan binding

7.61e−24

1.07e−19

2.78

6.84e−13

GO:0008201

Heparin binding

1.83e−21

1.44e−18

2.90

1.97e−09

  1. aRank-based enrichment test based on minimum significant difference identifies gene−sets that are over-represented among top-ranked genes without a directional hypothesis
  2. bGene−set enrichment analysis (GSEA) tests for over-representation in among top and bottom genes based on Log2 fold-changes in comparing time−points (Week 2 vs. Week 0 and Week 12 vs. Week 0). Positive normalized enrichment scores (NES) indicate genes with higher expression in Week 2/12 compared to Week 0; negative NES indicates genes with higher expression in Week 0 compared to Week 2/12
  3. cOver-representation tests based on differentially expressed genes. P-values are adjusted for FDR
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BMC Bioinformatics

ISSN: 1471-2105

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