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Table 4 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of murine diaphragms at 5 time points

From: Time-resolved transcriptional profiling of Trichinella-infected murine myocytes helps to elucidate host–pathogen interactions in the muscle stage

ID

Description

Gene ratio (%)

Bg ratio (%)

Enrich. factora

q-valueb

d-1, upregulated

 ko04668

TNF signaling pathway

11.56

1.37

8.44

2.06E−11

 ko04060

Cytokine-cytokine receptor interaction

10.98

3.19

3.45

0.000183

 ko04064

NF-kappa B signaling pathway

7.51

1.59

4.72

0.000183

 ko05144

Malaria

4.62

0.66

7.01

0.000626

 ko05202

Transcriptional misregulation in cancer

8.67

2.51

3.45

0.000914

 ko04621

NOD-like receptor signaling pathway

4.62

0.76

6.09

0.001182

 ko05132

Salmonella infection

5.20

1

5.23

0.001182

 ko05134

Legionellosis

4.62

0.83

5.55

0.001781

 ko04640

Hematopoietic cell lineage

5.78

1.37

4.22

0.002204

 ko05206

MicroRNAs in cancer

6.36

1.79

3.55

0.004319

 ko04933

AGE-RAGE signaling pathway in diabetic complications

5.20

1.27

4.1

0.004957

 ko04010

MAPK signaling pathway

8.67

3.27

2.65

0.007215

 ko04380

Osteoclast differentiation

5.78

1.67

3.47

0.007614

 ko04630

Jak-STAT signaling pathway

6.36

2.03

3.13

0.008884

 ko04066

HIF-1 signaling pathway

5.20

1.44

3.6

0.009357

 ko04920

Adipocytokine signaling pathway

4.05

0.91

4.45

0.009608

d-1, downregulated

 ko04974

Protein digestion and absorption

7.14

1.12

6.38

5.46E−06

 ko05150

Staphylococcus aureus infection

6.63

1.06

6.27

1.07E−05

 ko04612

Antigen processing and presentation

6.12

1.18

5.18

0.000166

 ko05321

Inflammatory bowel disease

5.10

0.83

6.12

0.000166

 ko05145

Toxoplasmosis

6.63

1.47

4.52

0.000166

 ko04512

ECM-receptor interaction

5.61

1.05

5.37

0.000166

 ko05310

Asthma

4.08

0.68

5.96

0.00131

 ko04672

Intestinal immune network for IgA production

4.59

0.90

5.12

0.001329

 ko04514

Cell adhesion molecules

7.14

2.13

3.36

0.001439

 ko05323

Rheumatoid arthritis

5.61

1.43

3.92

0.00198

 ko05152

Tuberculosis

7.65

2.53

3.03

0.002057

 ko05332

Graft-versus-host disease

4.08

0.78

5.21

0.002057

 ko04640

Hematopoietic cell lineage

5.10

1.37

3.73

0.004764

 ko04940

Type I diabetes mellitus

4.08

0.91

4.49

0.004971

d-3, upregulated

 ko04713

Circadian entrainment

13.89

1.19

11.62

0.004997

d-3, downregulated

 ko04974

Protein digestion and absorption

18.42

1.12

16.45

1.37E−05

 ko05144

Malaria

10.53

0.66

15.96

0.003842

 ko05143

African trypanosomiasis

10.53

0.71

14.84

0.003842

d-7, downregulated

 ko04512

ECM-receptor interaction

23.53

1.05

22.51

0.000396

 ko04974

Protein digestion and absorption

23.53

1.12

21.01

0.000396

 ko04510

Focal adhesion

23.53

2.60

9.05

0.00683

 ko04710

Circadian rhythm

11.76

0.35

33.76

0.009739

d-10, downregulated

 ko04974

Protein digestion and absorption

12.90

1.12

11.52

4.08E−05

 ko04512

ECM-receptor interaction

11.29

1.05

10.8

0.000179

 ko04932

Non-alcoholic fatty liver disease

12.90

1.94

6.65

0.000855

 ko05010

Alzheimer’s disease

12.90

2.24

5.76

0.001788

 ko00190

Oxidative phosphorylation

11.29

1.77

6.39

0.001807

 ko04151

PI3K-Akt signaling pathway

17.74

4.62

3.84

0.001807

 ko05012

Parkinson’s disease

11.29

1.84

6.13

0.001807

 ko05016

Huntington’s disease

12.90

2.48

5.21

0.001807

  1. KEGG pathway analysis identified signaling pathways over-represented in T. spiralis-infected mouse diaphragms (q-value < 0.01) compared to uninfected controls. Genes that were differentially expressed more than twofold were utilized as input with up- and downregulated genes considered respectively. For each enriched KEGG pathway, the ratio of DEGs in the pathway/all DEGs in all pathways (Gene ratio) and the ratio of genes in the pathway/all genes in all pathways (Bg ratio) are reported
  2. TNF Tumor necrosis factor, ECM extracellular matrix protein,NF nuclear factor, NOD nodulation, AGE–RAGE advanced glycation endproducts–receptor for advanced glycation endproducts, JAK–STAT Janus kinase-signal transducer and activator of transcription pathway, IgA immunoglobulin A, HIF-1 hypoxia-inducible factor 1, PI3K-Akt phosphatidylinositol 3-kinase/protein kinase B
  3. aEnrichment (Enrich.) factors show the proportion of gene ratio to Bg ratio. The bigger the enrichment factor, the more significant the pathway
  4. bq-value is the p-value adjusted by multiple hypothesis testing. The smaller the q-value, the more significant the pathway. The DEGs corresponding to the respective enriched KEGG pathway are shown in Additional file 3: Table S3
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