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Table 2 Selected differentially expressed genes between regenerating WT limb buds and non-regenerating transgenic N1 limb buds.

From: Identification of genes associated with regenerative success of Xenopus laevishindlimbs

Affymetrix Probeset(s)

Gene name

Array fold change

P- value

qPCR fold change

Regeneration or developmental role

Pathway/function

xl.22174.1.A1_at

Hypothetical protein MGC68766

3.85 WT

0.029

59.89

-

Homology to MHCIIα

xl.23895.2.S1_at

Nucleoplasmin 3*

3.54 WT

0.003

4.04

-

Chaperone

xl.23895.1.A1_at

 

2.63 WT

0.011

   

xl.24281.1.A1_at

Hsp90

3.13 WT

0.007

4.72

Muscle fibre regeneration [73]

Stress, chaperone

xl.16042.1.S1_at

Type IX collagen

2.94 WT

0.003

6.33

Bone formation and fracture [74]

Matrix, cartilage

xl.318.1.S1_at

Gremlin

2.85 WT

0.005

3.49

Limb development [31]

BMP inhibitor

xl.21917.1.S1_at

Microtubule associated protein 1 light chain 3 α

2.77 WT

0.003

1.52

 

Cytoskeletal protein

xl.6690.1.S1_at

TIM22

2.70 WT

0.008

1.92

-

Mitochondria transport

xl.17389.1.S1_at

Tiarin

2.70 WT

0.029

2.48

-

Early patterning

xl.8219.1.S1_at

Hsp60*

2.70 WT

0.286

2.62

Zebrafish no blastema (nbl) mutant [35]

Stress, chaperone

xl.8219.2.S1_at

 

1.81 WT

0.045

   

xl.23194.1.S1_at

 

2.31 WT

0.049

   

xl.24730.1.S1_at

 

2.11 WT

0.014

   

xl.24730.1.S1_a_ at

 

1.94 WT

0.024

   

xl.16470.1.A1_at

3' exoribonuclease

2.56 WT

0.040

3.66

 

RNA binding

xl.21891.1.S1_at

Alcohol dehydrogenase 1

9.7 N1

0.002

8.73

-

Retinoic acid synthesis

xl.7740.1.A1_at

COX-2

8.14 N1

0.048

5.54

Up-regulated in injured growth plate [75]

Inflammation

xl.9871.1.A1_s_a t

Thrombospondin 4*

7.32 N1

0.001

9.69

Expressed during osteogenesis [76]

Secreted, regulates cell interactions

xl.12952.1.S1_at

 

N1 only

<0.001

   

xl.11387.1.S1_at

Haemoglobin α

7.16 N1

0.004

6.23

-

Oxygen transport

xl.16451.1.A1_at

Transmembrane serine protease 2

6.96 N1

0.001

4.69

-

Protease

xl.9576.1.S1_at

Carbonic anhydrase II

6.52 N1

0.010

3.25

 

Metabolic enzyme

xl.8949.1.S1_at

Ornithine decarboxylase 2

4.48 N1

0.001

3.46

-

Metabolic enzyme

xl.2784.1.S1_at

Metallothionien A*

4.24 N1

0.023

4.20

Up-regulated in liver regeneration [77]. Up- regulated in skin wound healing [78]

Binds Zinc and Copper

xl.3144.1.S1_s_at

 

N1 only

0.048

   

xl.3144.1.S1_at

 

N1 only

0.026

   

xl.6874.1.S1_at

Keratin 18

N1 only

<0.001

4.31

-

Intermediate filament

xl.8908.1.S1_at

Raldh2*

3.01 N1

0.004

3.79

-

Retinoic acid synthesis

xl.18999.1.A1_at

 

N1 only

0.009

   
  1. Genes were selected from lists of up-regulated >2 fold in WT (regenerating, top section) or N1 (non-regenerating, lower section) and are listed in the order from the most differentially expressed according to Affymetrix GeneChip analysis (Array fold change, based on the mean of the two biological replicate samples). WT only or N1 only indicates that after normalisation of the array data, only WT or N1 samples respectively were called present by the GCOS software. P values were calculated for differential expression using AffylmGUI [28]. All the genes shown have been verified with qPCR and mean (from triplicate samples) normalised fold change values are shown (qPCR fold change). *denotes genes with 2 or more probesets on the chip, in each case all are up-regulated in the same direction. Where a known role in development or regeneration can be identified, representative references are given.
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BMC Developmental Biology

ISSN: 1471-213X

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