Table 2 Functional analysis of significantly differentially expressed genes (FDR < 0.01; LogFC = 1)

MSC[Naive] vs MSC[In vitro]

Down

Cell-cycle regulation and progression

2.1e−04

2.3e−03

DNA recombination/metabolic process

3.6e−04

2.9e−03

Chromosome (condensed)

1.7e−06

5.5e−03

DNA repair and response to stress

1.9e−04

1.9e−03

Up

Immune system response

1.2e−05

7.6e−05

Signaling pathway

3.3e−04

3.7e−06

Cytokine production and response

7.1e−05

3.4e−04

Cellular response to stress and stimuli

1.3e−05

1.2e−05

Metabolic process

2.4e−04

2.3e−05

Protein modification/assembly/transport

6.4e−05

3.4e−05

Ion transport and homeostasis

5.9e−06

3.4e−06

Cell migration and chemotaxis

8.1e−05

8.9e−07

Trans (cell) membrane transport

9.0e−04

9.8e−05

Ubiquitination and apoptosis

2.0e−04

8.8e−05

Signal transduction

9.9e−08

4.5e−06

Tissue development and regeneration

1.3e−04

8.1e−06

Biosynthetic process

1.2e−03

8.5e−04

Cell-cell adhesion

1.1e−05

3.7e−06

Phagocytosis and endocytosis

1.7e−05

1.0e−03

Catabolic process

1.0e−03

4.1e−04

Regulation of (cell) proliferation

1.8e−05

1.7e−04

Cell membrane activity

4.0e−07

2.9e−05

Regulation of (cell) differentiation

7.4e−04

7.5e−07

Synaptic function and activity

3.1e−03

7.1e−04

Cell and tissue morphology

1.2e−03

5.6e−04

Receptor binding

1.3e−03

6.8e−03

Transcriptional activity

2.8e−03

1.2e−02

I-kappaB kinase/NF-kappaB signaling

2.6e−04

2.3e−03

Regulation of (cell) activation

0.0e+00

1.4e−03

Regulation of cell homeostasis

1.5e−03

9.1e−04

MSC[SCI] vs MSC[In vitro]

Down

Cell-cycle regulation and progression

1.3e−04

3.8e−03

DNA recombination/metabolic process

2.2e−04

9.6e−03

Chromosome (condensed)

6.1e−08

8.9e−03

DNA repair and response to stress

1.2e−05

5.1e−03

Meiotic cell-cycle process

7.5e−05

1.1e−02

Up

Immune system response

2.5e−05

2.6e−04

Cellular response to stress and stimuli

1.7e−05

5.9e−05

Signaling pathway

3.5e−04

4.9e−05

Cytokine production and response

6.5e−05

7.1e−04

Metabolic process

7.0e−04

2.0e−04

Ion transport and homeostasis

4.2e−07

1.4e−05

Protein modification/assembly/transport

3.2e−04

1.2e−04

Trans (cell) membrane transport

4.0e−04

1.4e−04

Cell migration and chemotaxis

1.1e−04

9.9e−05

Signal transduction

2.8e−06

5.5e−05

Tissue development and regeneration

2.1e−04

1.7e−06

Ubiquitination and apoptosis

6.5e−04

3.3e−04

Biosynthetic process

1.0e−03

1.1e−03

Cell-cell adhesion

3.1e−05

1.9e−05

Synaptic function and activity

2.1e−04

3.7e−05

Phagocytosis and endocytosis

1.7e−05

1.7e−03

Microtubuli and cytoskeleton

6.1e−04

2.7e−02

Cell membrane activity

3.1e−06

1.1e−04

Regulation of (cell) proliferation

2.6e−05

1.8e−04

Regulation of (cell) differentiation

1.5e−03

1.3e−05

Transcriptional activity

3.0e−03

1.6e−04

Catabolic process

5.5e−03

1.3e−03

Cell and tissue morphology

4.6e−03

2.3e−05

Regulation of (cell) activation

5.0e−10

2.2e−03

I-kappaB kinase/NF-kappaB signaling

5.9e−04

2.3e−03

Secretion

2.3e−03

1.8e−04

Neuronal cell activity

2.4e−07

2.7e−05

Sensory perception process

1.8e−03

4.7e−05

MSC[SCI] vs MSC[Naive]

Up

Tissue development and regeneration

8.7e−04

6.3e−04

Cell morphology

9.6e−04

9.6e−04