Table 1 Functional analysis of the switched genes across stages of differentiation/development

From: Not just a colourful metaphor: modelling the landscape of cellular development using Hopfield networks

Case study

#Selected probes

Transition

# Probes switched

Biological process

P-value

KEGG pathways

P-value

GSE13201

3,753

P7–P4

3,405

Cell fate determination

7.72E−03

Hedgehog signalling pathway

1.3E−2

  

P5–P4

1,861

Cellular differentiation

1.34E−09

Wnt signalling pathway

8.0E−2

  

P6–P4

3,430

System development

9.96E−12

Basal cell carcinoma

1.3E−2

  

P6–P5

2,712

Skeletal system development

1.77E−10

  
  

P7–P5

2,810

Central nervous system development

1.10E−09

  
  

P7–P6

1,453

Embryo development

9.54E−09

  

GSE8091

2,748

E9–E13

2,594

System development

3.48E−06

Focal adhesion

8.1E−3

  

E9–E11

2,169

Developmental process

1.06E−05

  
  

E11–E13

2,430

Cell differentiation

1.14E−04

  

THP1-Mac

45

0–96 h

20

Cell differentiation

6.57E−13

Wnt signalling pathway

7.2E−5

  

0–1 h

23

System development

1.05E−11

B-cell receptor signalling pathway

1.5E−3

  

0–6 h

22

Haemopoiesis

4.88E−10

PPAR signalling pathway

1.9E−2

  

1–6 h

23

  

MAPK signalling pathway

4.8E−2

  

1–96 h

21

    
  

1–6 h

23

    
  

6–96 h

22

    

GSE17708

2,620

0–72 h

1,974

Regulation of cell proliferation

1.82E−02

ECM-receptor interaction

7.1E−3

  

0–8 h

1,511

Cell adhesion

1.80E−3

  
  

0–16 h

2,013

Developmental process

4.40E−01

  
  

0–24 h

2,021

    
  

8–16 h

1,806

    
  

16–24 h

1,606

    
  

16–72 h

1,737

    
  

8–24 h

1,936

    
  

24–72 h

1,478

    
  

8–72 h

1,960

    
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