Supplemental Data
Expression changes and bioinformatic analysis of rat Wallerian
degeneration after sciatic nerve injury
Dengbing Yao1, 2#, Meiyuan Li1#, Dingding Shen1, Fei Ding1, Shibi Lu3, Qing Zhao3*,
Xiaosong Gu1*
1
Jiangsu Key Laboratory of Neuroregeneration, 2School of Life Sciences, Nantong
University, Nantong, Jiangsu 226019, China
Key Laboratory of People’s Liberation Army, Institute of Orthopaedics, Chinese PLA
General Hospital, Beijing 100853, China
3
Table S1. Primers used in real-time qRT-PCR assays
Gene
Primers (5’–3’)
Length
Spp1-FP
Spp1-RP
AACAGTATCCCGATGCCACA
TTCCCGTTGCTGTCCTGAT
130bp
Tnc-FP
Tnc-RP
AGGGAGACAAGGAGGGCG
TTGAGGCGGTAACGATCAAA
148bp
Thbs4-FP
Thbs4-RP
AAATACCATCCCTGCTACCCT
TTGTTTGTTTTGGCAAAGTTG
131bp
Prkcq-FP
Prkcq-RP
AGGCCGAATGCTAATGAATG
GGTGGCTGTGAACTCGTGAC
160bp
Col5a1-FP
Col5a1-RP
TGAAGGGTGAGCCAGGAGA
GCCTCTGGCACCATCACTC
116bp
Cldn14-FP
Cldn14-RP
AGACCACCTTCGCGGTGTT
TGGGCAGCAGAGGGTTGTA
120bp
Cldn15-FP
Cldn15-RP
CGGGCAGAAGCAATCAGAC
AAGACTGAGGAGGGAGAAGGTT
93bp
Ctnna2-FP
Ctnna2-RP
GGTGTATGATGGTGTTCGGG
GCTGGTCATCCTCGGTCTG
Birc3-FP
Birc3-RP
CCCTGAATCCAGCCAACA
AGGAGCCACTGAAGTAGCCA
Mapk3-FP
GACCAGAGTGGCTATCAAGAAG
140bp
120bp
Mapk3-RP
TGGGTGCTCTGAGGATGTCT
137bp
Itga6-FP
Itga6-RP
GGCTACTCAATCGCTGGGA
GATTTCTGGCGGAGGTCAA
164bp
Ccr1-FP
Ccr1-RP
GGGAACTTTGAGGTCGCTTAG
GCCCAAGCCACTCATTATCC
127bp
Bid-FP
Bid-RP
GGTTTACCTGGAGGGGGAC
GCCTGGCAATGTTGTGGA
131bp
Acvr1c-FP
Acvr1c-RP
GACATCTATTCGGTGGGGCT
AACGACCTTCCTCATTTCCTCT
138bp
Itga11-FP
Itga11-RP
GAACCACGCCGCATACCT
TCTGCTCGCCCCGAAGA
170bp
Cacna1c-FP
Cacna1c-RP
GGTGGAAGCGGTCTTGATTT
AGGATGTTGTCTGCGGCG
138bp
Table S2. The 23 types of significant differentially expression tendencies during WD
1
day
-1
4
days
-2
7
days
-3
14
days
-3
21
days
-3
28
days
-2
Genes_Assigned*
54
0
day
0
175
6.80119
4.67E-177
83
0
1
2
3
2
2
3
677
231.0492
1.42E-132
47
0
1
2
3
3
3
2
139
14.94167
1.78E-83
95
0
-1
-2
-2
-2
-2
-3
310
92.59444
2.90E-72
49
0
-1
-2
-3
-3
-3
-3
73
6.580952
1.28E-49
64
0
-1
-2
-2
-3
-3
-2
108
20.93135
1.77E-41
46
0
0
1
2
3
4
3
304
128.023
4.67E-41
12
0
1
2
3
4
4
3
40
2.193254
5.65E-36
36
0
1
2
3
3
3
3
70
9.932937
2.17E-35
88
0
-1
-2
-2
-3
-2
-2
178
68.26746
6.39E-29
41
0
-1
-2
-3
-4
-3
-2
91
23.67976
4.13E-26
90
0
0
-1
-2
-3
-3
-2
213
107.9556
1.20E-19
87
0
-1
-2
-3
-2
-2
-2
178
100.8587
1.57E-12
62
0
-1
-2
-3
-3
-2
-2
81
34.40238
8.19E-12
77
0
1
2
3
3
2
2
139
79.21667
5.92E-10
28
0
1
2
3
3
4
3
24
5.248016
1.98E-09
86
0
-1
-1
-2
-3
-3
-2
179
112.8298
3.89E-09
58
0
-1
-2
-2
-3
-3
-3
21
4.269444
5.73E-09
73
0
1
2
2
3
3
3
45
18.95198
2.44E-07
79
0
1
2
2
3
3
2
199
137.3369
3.37E-07
69
0
-1
-2
-2
-3
-2
-3
88
56.46944
5.67E-05
70
0
-1
-2
-2
-2
-3
-3
25
10.26905
6.95E-05
91
0
-1
-2
-2
-2
-3
-2
190
143.4036
9.59E-05
No.
Genes_Expected#
P_value
No. represents the serial number of the significant tendency and has no special meaning. The values of
0, ±1, ±2, ±3 do not mean the actual value of gene expression, but are rather the classification marks
of the expression change. *Genes assigned represents the actual number of the differential genes in
this tendency; #genes expected represents the theoretical gene number in this tendency under random
distribution; P-value represents the significance of the difference between the actual gene number and
the theoretical gene number under random distribution. The smaller the P value, the more significant
the effect of WD progression on the gene expression tendency. Gene symbol means the official gene
symbol in the NCBI GenBank.
Table S3. The significant pathways of differentially expressed genes during WD
Path_Id
5010
4740
4514
4010
4110
4512
4310
4670
4060
4510
5016
620
4810
4530
982
4640
3320
10
330
4610
310
4115
4920
4520
3030
910
Path_Name
Alzheimer's disease
Olfactory transduction
Cell adhesion molecules (CAMs)
MAPK signaling pathway
Cell cycle
ECM-receptor interaction
Wnt signaling pathway
Leukocyte transendothelial migration
Cytokine-cytokine receptor interaction
Focal adhesion
Huntington's disease
Pyruvate metabolism
Regulation of actin cytoskeleton
Tight junction
Drug metabolism - cytochrome P450
Hematopoietic cell lineage
PPAR signaling pathway
Glycolysis / Gluconeogenesis
Arginine and proline metabolism
Complement and coagulation cascades
Lysine degradation
p53 signaling pathway
Adipocytokine signaling pathway
Adherens junction
DNA replication
Nitrogen metabolism
P-Value
4.16E-26
3.08E-22
1.7E-21
2.24E-19
9.58E-16
1.33E-13
1.51E-13
1.51E-12
1.4E-11
1.6E-11
4.94E-11
1.52E-10
2.45E-10
7.19E-10
2.84E-09
3.78E-09
7.98E-09
1.23E-08
2.01E-08
4.23E-08
5.64E-08
6.06E-08
8.53E-08
9.2E-08
1.4E-07
1.54E-07
FDR
1.63E-24
6.05E-21
2.22E-20
2.2E-18
7.52E-15
7.74E-13
8.49E-13
7.39E-12
5.64E-11
6.27E-11
1.76E-10
4.94E-10
7.39E-10
2.02E-09
7.24E-09
9.27E-09
1.84E-08
2.67E-08
4.15E-08
8.04E-08
1.02E-07
1.08E-07
1.42E-07
1.5E-07
2.15E-07
2.33E-07
Enrichment
10.5547
0.102848
4.101403
3.13759
3.853352
4.591622
3.469557
3.56221
2.753148
2.839546
6.165363
6.211033
2.647499
3.072302
3.985689
3.700997
3.812399
4.527223
5.480323
3.653549
5.937017
3.382915
3.653549
3.416305
4.615009
7.307097
760
4650
4620
4360
4664
4350
5216
4612
340
5212
380
5210
4020
4630
4912
4930
590
230
4614
4080
5014
4916
980
5332
4940
4070
5215
5217
4012
260
2010
650
53
562
640
1040
561
4662
5219
564
5330
533
5218
600
280
5214
4720
71
Nicotinate and nicotinamide metabolism
Natural killer cell mediated cytotoxicity
Toll-like receptor signaling pathway
Axon guidance
Fc epsilon RI signaling pathway
TGF-beta signaling pathway
Thyroid cancer
Antigen processing and presentation
Histidine metabolism
Pancreatic cancer
Tryptophan metabolism
Colorectal cancer
Calcium signaling pathway
Jak-STAT signaling pathway
GnRH signaling pathway
Type II diabetes mellitus
Arachidonic acid metabolism
Purine metabolism
Renin-angiotensin system
Neuroactive ligand-receptor interaction
Amyotrophic lateral sclerosis (ALS)
Melanogenesis
Metabolism of xenobiotics by cytochrome P450
Graft-versus-host disease
Type I diabetes mellitus
Phosphatidylinositol signaling system
Prostate cancer
Basal cell carcinoma
ErbB signaling pathway
Glycine, serine and threonine metabolism
ABC transporters
Butanoate metabolism
Ascorbate and aldarate metabolism
Inositol phosphate metabolism
Propanoate metabolism
Biosynthesis of unsaturated fatty acids
Glycerolipid metabolism
B cell receptor signaling pathway
Bladder cancer
Glycerophospholipid metabolism
Allograft rejection
Keratan sulfate biosynthesis
Melanoma
Sphingolipid metabolism
Valine, leucine and isoleucine degradation
Glioma
Long-term potentiation
Fatty acid metabolism
4.41E-07
4.67E-07
5.99E-07
6.55E-07
2.15E-06
2.3E-06
2.52E-06
2.75E-06
3.36E-06
3.52E-06
4.43E-06
5.32E-06
6.15E-06
6.67E-06
6.82E-06
7.96E-06
1.23E-05
1.85E-05
1.96E-05
2.26E-05
2.96E-05
3.19E-05
3.23E-05
3.41E-05
6.68E-05
8.53E-05
0.000134
0.000136
0.000149
0.000184
0.000208
0.000221
0.000226
0.000244
0.00031
0.000318
0.000499
0.000588
0.000652
0.000678
0.000725
0.000892
0.001101
0.001199
0.001364
0.001475
0.001523
0.001712
6.12E-07
6.43E-07
7.95E-07
8.56E-07
2.55E-06
2.7E-06
2.92E-06
3.14E-06
3.7E-06
3.84E-06
4.65E-06
5.39E-06
6.04E-06
6.42E-06
6.53E-06
7.43E-06
1.11E-05
1.6E-05
1.69E-05
1.91E-05
2.39E-05
2.54E-05
2.56E-05
2.67E-05
5.09E-05
6.38E-05
9.57E-05
9.7E-05
0.000106
0.000126
0.00014
0.000147
0.00015
0.00016
0.000197
0.000201
0.000305
0.000353
0.000387
0.000401
0.000424
0.000513
0.000619
0.000667
0.000746
0.000797
0.000819
0.000908
7.58814
2.868206
2.968508
2.617468
3.196855
3.001129
4.5964
2.824909
5.768761
3.110454
3.914516
2.798463
2.169874
2.369869
2.832527
3.578986
3.327339
2.37208
5.480323
1.931761
4.765498
2.598916
3.247599
3.105516
2.859299
2.911422
2.501887
3.044624
2.548987
3.461257
3.653549
3.914516
7.829033
3.372506
3.779533
4.110242
3.349086
2.517986
3.25857
3.058785
2.651769
4.513207
2.470005
3.523065
3.014178
2.491056
2.402333
2.940661
4540
350
5211
240
641
5220
4340
5222
5320
480
4910
830
565
591
4730
3010
960
5340
670
190
410
3430
791
4660
4120
5310
72
903
51
983
52
5223
500
4130
Gap junction
Tyrosine metabolism
Renal cell carcinoma
Pyrimidine metabolism
3-Chloroacrylic acid degradation
Chronic myeloid leukemia
Hedgehog signaling pathway
Small cell lung cancer
Autoimmune thyroid disease
Glutathione metabolism
Insulin signaling pathway
Retinol metabolism
Ether lipid metabolism
Linoleic acid metabolism
Long-term depression
Ribosome
Alkaloid biosynthesis II
Primary immunodeficiency
One carbon pool by folate
Oxidative phosphorylation
beta-Alanine metabolism
Mismatch repair
Atrazine degradation
T cell receptor signaling pathway
Ubiquitin mediated proteolysis
Asthma
Synthesis and degradation of ketone bodies
Limonene and pinene degradation
Fructose and mannose metabolism
Drug metabolism - other enzymes
Galactose metabolism
Non-small cell lung cancer
Starch and sucrose metabolism
SNARE interactions in vesicular transport
0.00231
0.002722
0.002803
0.003215
0.003862
0.004067
0.004224
0.004374
0.005012
0.005185
0.005603
0.006808
0.008981
0.011506
0.01155
0.011936
0.01197
0.012297
0.012491
0.012967
0.014474
0.014474
0.016643
0.021461
0.021736
0.023794
0.02457
0.027024
0.027083
0.032617
0.03932
0.040364
0.045089
0.045089
0.001196
0.001387
0.001423
0.001607
0.001884
0.001969
0.002033
0.002093
0.002354
0.002423
0.002587
0.003089
0.003952
0.004891
0.004907
0.005045
0.005057
0.005173
0.005241
0.005406
0.005917
0.005917
0.00672
0.008433
0.008528
0.00923
0.009491
0.010301
0.01032
0.012228
0.014458
0.014798
0.016311
0.016311
2.192129
3.182123
2.34871
2.248338
6.263226
2.141735
2.52938
2.076754
2.221753
2.740162
1.853639
2.223899
3.196855
3.068981
2.102042
0.144219
4.871398
2.595942
3.914516
0.431037
3.288194
3.288194
10.96065
1.826774
1.704989
2.989267
5.480323
3.985689
2.645673
2.24195
3.044624
2.068046
2.248338
2.248338
Path Id means the index serial number of the pathway in the KEGG database; Path name means the
entry name of the pathway in the KEGG database; Path different gene count means the number of
differential genes contained in the pathway in the KEGG database; Path gene count means the total
amount of genes contained in the pathway in the KEGG database; P value represents the significance
of the pathway (according to the KEGG classification standards), the lower the P value the more
significant the pathway; when P value is below 0.05 the pathway is significant. FDR represents false
detection rate, the smaller FDR is the smaller the judgment error of the significance of the pathway.
Enrichment represents the enrichment of the pathway, with the same P value, the larger the
enrichment is the more important the pathway.