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Table 2 Top 20 enriched biological processes. Gene enrichment was performed using over-representation analysis with NetworkAnalyst [33]

From: The symbiotic relationship between Caenorhabditis elegans and members of its microbiome contributes to worm fitness and lifespan extension

Pathways

Worms grown with Chryseobacterium sp. CHNTR56 MYb120

Rank

Hits/Total

P.Value

Worms grown with Comamonas sp. 12022 MYb131

Rank

Hits/Total

P.Value

Behaviour

Locomotory behavior

10

16/40

0.0077

–

–

–

–

Biological phase

M phase of mitotic cell cycle

13

4/5

0.00964

–

–

–

–

Biological regulation

Regulation of sequence specific DNA binding transcription factor activity

9

10/20

0.00536

Regulation of sequence specific DNA binding transcription factor activity

18

7/20

0.00561

Cellular component organization or biogenesis

Protein oligomerization

2

20/39

5.51E-05

Protein oligomerization

19

10/39

0.0118

Protein homooligomerization

3

19/37

8.26E-05

–

 

–

–

Chromosome condensation

7

7/11

0.0035

–

 

–

–

Cellular process

Dephosphorylation

4

48/140

0.00052

Dephosphorylation

2

46/140

1.7E-11

Protein dephosphorylation

1

48/121

7.6E-06

Protein dephosphorylation

1

46/121

4.1E-14

Negative regulation of nucleobase containing compound metabolic process

14

25/73

0.0108

Phosphorylation

9

86/504

0.00013

Neuropeptide signaling pathway

17

9/19

0.0126

Protein phosphorylation

5

86/470

8.7E-06

Developmental process

–

–

–

–

Nervous system development

16

50/286

0.00193

–

–

–

–

Neurogenesis

15

47/262

0.00152

–

–

–

–

Generation of neurons

14

47/260

0.00129

–

–

–

–

Neuron differentiation

12

44/230

0.00055

–

–

–

–

Neuron development

11

41/207

0.0004

–

–

–

–

Neuron projection development

13

37/192

0.00128

–

–

–

–

Epithelial cell differentiation

6

13/30

1.2E-05

–

–

–

–

Epidermis development

20

7/23

0.013

–

–

–

–

Mesoderm development

17

10/31

0.00195

Metabolic process

DNA replication

20

21/62

0.021

–

   

DNA replication initiation

6

5/6

0.00252

Macromolecule modification

4

147/896

3.9E-06

Negative regulation of RNA metabolic process

11

22/61

0.00838

Protein modification process

3

146/848

2.3E-07

Negative regulation of transcription, DNA dependent

12

22/61

0.00838

–

 

–

–

Negative regulation of transcription from RNA polymerase II promoter

18

16/43

0.0167

–

 

–

–

Multicellular organismal process

Detection of stimulus involved in sensory perception

8

6/9

0.00509

–

 

–

–

Regulation of muscle contraction

19

9/20

0.0185

–

 

–

–

Multi-organism process

Spermatid differentiation

16

7/13

0.012

Spermatid differentiation

8

8/13

2.5E-05

Spermatid development

15

7/13

0.012

Spermatid development

7

8/13

2.5E-05

Response to stimulus

Detection of stimulus

5

8/13

0.00238

Response to wounding

10

7/12

0.00013

  1. Enriched biological processes ranked by P-value and categorised based on an online resource (Mouse Genome Informatics, https://www.informatics.jax.org/) are shown