Table 1

Top 25 up- and downregulated genes for the microarray comparison of notochordal cell (NC)-rich nucleus pulposus (NP) (reference) vs. chondrocyte-like cell-(CLC)-rich NP in chondrodystrophic dogs

Chondrodystrophic dogs: NC-rich NP vs. CLC-rich NP


Total upregulated genes: 1.178

Total downregulated genes: 1,741


Description

GO term: biological Process

N-fold change

P-value


Carboxypeptidase E

Protein modification process

8.65

8.65E-05

Transferrin

Transferrin transport

8.58

1.56E-02

Ceruloplasmin (ferroxidase)

Cellular iron ion homeostasis

7.34

2.02E-03

Frizzled-related protein

Negative regulation of canonical Wnt receptor signaling pathway

7.26

4.24E-03

Decorin

Peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan

7.11

2.00E-02

Cartilage oligomeric matrix protein

Anti-apoptosis

7.08

6.69E-05

Serglycin

Negative regulation of bone mineralization

6.97

9.64E-03

Lumican

Collagen fibril organization

6.88

1.39E-02

Not annotated

Not annotated

6.66

1.15E-02

Metallothionein 2A

Cellular response to erythropoietin

6.60

5.33E-03

RAN binding protein 3-like

Intracellular transport

6.54

4.71E-02

Retinol binding protein 4, plasma

Protein complex assembly

6.40

6.79E-04

Cysteine dioxygenase, type I

Response to glucagon stimulus

6.30

1.36E-02

Adenylate cyclase 2

Activation of adenylate cyclase activity by G-protein signaling pathway

5.97

3.94E-04

Tetraspanin 13

Not available

5.88

1.95E-02

Microfibrillar associated protein 5

Not available

5.75

1.17E-04

Proteoglycan 4

Cell proliferation

5.61

3.00E-03

S100 calcium binding protein A12

Inflammatory response

5.59

1.15E-02

Phosphotyrosine interaction domain containing 1

Not available

5.57

8.41E-05

Nephronectin

Cell differentiation

5.54

2.76E-04

Lysozyme

Cell wall macromolecule catabolic process

5.47

2.42E-02

SPARC-like 1 (hevin)

Signal transduction

5.34

2.85E-02

Glycoprotein 25L

Not available

5.27

5.84E-04

Serpin peptidase inhibitor, clade G (C1 inhibitor), member 1

Regulation of proteolysis

5.08

6.92E-04

Sphingomyelin phosphodiesterase, acid-like 3A

Sphingomyelin catabolic process

5.01

1.16E-02

Keratin 18

Golgi to plasma membrane CFTR protein transport

-12.93

1.44E-03

tRNA-yW synthesizing protein 3 homolog

tRNA processing

-7.83

9.45E-04

A kinase (PRKA) anchor protein 12

Signal transduction

-7.69

7.56E-03

Phospholipase C-like 1

Lipid metabolic process

-7.40

9.48E-03

Desmocollin 3

Cell adhesion

-7.05

1.40E-03

Myosin, light chain 9, regulatory

Regulation of muscle contraction

-6.84

1.64E-02

Mitochondrial ribosomal protein S27

Not available

-6.76

4.96E-04

Ectonucleotide pyrophosphatase/phosphodiesterase 2

Regulation of cell migration

-6.41

9.38E-03

Keratin 19

Cell differentiation involved in embryonic placenta development

-6.32

6.00E-03

Plakophilin 2

Carbohydrate metabolic process

-6.13

6.02E-04

Tetraspanin 7

Interspecies interaction between organisms

-6.01

3.00E-03

Keratin 8

Cytoskeleton organization

-5.94

2.60E-02

Nucleosome assembly protein 1-like 1

DNA replication

-5.92

1.40E-03

RAB20, member RAS oncogene family

Small GTPase mediated signal transduction

-5.79

2.91E-03

Caldesmon 1

Positive regulation of protein binding

-5.68

3.60E-03

Potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3

Synaptic transmission

-5.64

4.46E-03

Apelin

Positive regulation of phosphorylation

-5.59

7.66E-03

Sorbin and SH3 domain containing 2

Biological process

-5.42

3.39E-03

Phosphatidylcholine transfer protein

Cholesterol metabolic process

-5.37

1.30E-03

Kv channel interacting protein 1

Synaptic transmission

-5.14

< 1.0E-06

Carbonic anhydrase II

Carbon utilization

-5.07

2.57E-02

Thy-1 cell surface antigen

Cytoskeleton organization

-4.74

1.10E-02

RAB38, member RAS oncogene family

GTP catabolic process

-4.71

5.79E-04

Sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C

Neural tube development

-4.58

1.01E-04

Desmocollin 2

Cell adhesion

-4.48

9.91E-03


This specific comparison was chosen to illustrate the overall trend in gene regulations observed in early IVD degeneration. For the top 50 up- and downregulations of all performed microarray analyses, see Additional file 4. For brevity, only one Gene Ontology (GO)-term is given for each gene (obtained with bioDBnet [97]).

Smolders et al. Arthritis Research & Therapy 2013 15:R23   doi:10.1186/ar4157

Open Data