Table 2 Selected upregulated pathways in NCMs and UM cells, respectively (P < 0.05). A full list can be found in Additional file 6

Upregulated in NCMs

Metabolism

143

25.9

1.30E − 13

1.60E − 10

Complex I biogenesis

17

3.1

1.70E − 10

1.00E − 07

Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins

20

3.6

2.50E − 07

7.90E − 05

Respiratory electron transport

18

3.3

2.50E − 07

7.90E − 05

Cholesterol biosynthesis

10

1.8

3.50E − 07

8.80E − 05

The citric acid (TCA) cycle and respiratory electron transport

23

4.2

8.60E − 07

1.80E − 04

Regulation of cholesterol biosynthesis by SREBP (SREBF)

12

2.2

5.00E − 06

8.90E − 04

Activation of gene expression by SREBF (SREBP)

10

1.8

2.00E − 05

3.20E − 03

Metabolism of lipids

50

9.1

7.70E − 05

1.10E − 02

Response to elevated platelet cytosolic Ca2 + 

16

2.9

1.50E − 04

1.90E − 02

Localization of the PINCH-ILK-PARVIN complex to focal adhesions

4

0.7

2.10E − 04

2.30E − 02

Platelet degranulation

15

2.7

3.40E − 04

3.50E − 02

Cell-extracellular matrix interactions

6

1.1

4.20E − 04

4.00E − 02

Apoptotic execution phase

9

1.6

6.60E − 04

5.80E − 02

RHO GTPase cycle

32

5.8

8.00E − 04

6.60E − 02

Innate immune system

61

11.1

9.20E − 04

7.10E − 02

Metabolism of steroids

15

2.7

2.00E − 03

1.20E − 01

Membrane trafficking

38

6.9

5.10E − 03

2.50E − 01

Cell junction organization

11

2

6.90E − 03

3.10E − 01

Vesicle-mediated transport

39

7.1

7.80E − 03

3.30E − 01

Cell–cell communication

13

2.4

8.50E − 03

3.30E − 01

Metabolism of carbohydrates

21

3.8

8.50E − 03

3.30E − 01

Apoptosis induced DNA fragmentation

4

0.7

1.10E − 02

4.00E − 01

Apoptotic cleavage of cellular proteins

6

1.1

1.30E − 02

4.40E − 01

Immune system

95

17.2

1.40E − 02

4.40E − 01

Programmed cell death

16

2.9

1.50E − 02

4.50E − 01

Fatty acid metabolism

14

2.5

1.60E − 02

4.90E − 01

Signaling by VEGF

10

1.8

2.00E − 02

5.30E − 01

Integrin cell surface interactions

8

1.4

4.10E − 02

9.00E − 01

Biological oxidations

15

2.7

4.10E − 02

9.00E − 01

Upregulated in UMs

Metabolism of RNA

27

14.1

1.40E − 07

9.70E − 05

Processing of capped intron-containing pre-mRNA

13

6.8

1.10E − 04

3.80E − 02

Translation

12

6.3

5.70E − 04

1.10E − 01

mRNA splicing—major pathway

10

5.2

6.70E − 04

1.10E − 01

tRNA aminoacylation

4

2.1

1.30E − 02

1.00E + 00

Cellular response to heat stress

5

2.6

2.00E − 02

1.00E + 00

Major pathway of rRNA processing in the nucleolus and cytosol

7

3.7

2.10E − 02

1.00E + 00

Mitochondrial translation

5

2.6

2.30E − 02

1.00E + 00

RHOJ GTPase cycle

4

2.1

2.60E − 02

1.00E + 00

rRNA processing in the nucleus and cytosol

7

3.7

2.60E − 02

1.00E + 00

Metabolism of nucleotides

5

2.6

2.80E − 02

1.00E + 00

HIV life cycle

6

3.1

2.90E − 02

1.00E + 00

Metabolism of amino acids and derivatives

10

5.2

3.10E − 02

1.00E + 00

rRNA processing

7

3.7

3.20E − 02

1.00E + 00

rRNA modification in the nucleus and cytosol

4

2.1

3.40E − 02

1.00E + 00

Insulin-like growth factor-2 mRNA binding proteins (IGF2BPs/IMPs/VICKZs) bind RNA

2

1

3.40E − 02

1.00E + 00

Regulation of TP53 activity

6

3.1

3.80E − 02

1.00E + 00

ATF4 activates genes in response to endoplasmic reticulum stress

3

1.6

3.90E − 02

1.00E + 00