Title:Effects of Low-Level Laser Irradiation on Mesenchymal Stem Cells Proliferation: A Microarray Analysis

Lasers in Medical Science

Authors: Yihe Wu, M.D., Jue Wang, M.D., Dingxu Gong, M.D., Haiyong Gu, M.D., Ph.D., Shengshou Hu, M.D.and Hao Zhang, M.D., Ph.D.*

* Corresponding author: Hao Zhang, M.D.,Ph.D. E-mail:

Online Resource 1 Differentially expressed genes of MSCs upon LLLI

Gene symbol / Gene ID / Description / Fold change / P-value
1. Proliferation
Ddr2
Ccnd1
Map2k5
Wdr12
Gnb2
Ptpn6 / 685781
58919
29568
363237
81667
116689 / Discoidin domain receptor tyrosine kinase 2
cyclin D1
mitogen activated protein kinase kinase 5
WD repeat domain 12
guanine nucleotide binding protein (G protein), beta polypeptide 2
protein tyrosine phosphatase, non-receptor type 6 / 1.23661
1.20013
-1.22106
-1.23096
-1.23352
-1.26282 / 0.0304
0.0327
0.0293
0.0270
0.0127
0.0385
2. Apoptosis
Pik3ca
Nol3
Aven
Atg5
Dnase2a
Stk17b
Vdac1
Akt1
Rhoa
Ada / 170911
85383
311299
365601
171575
170904
83529
24185
117273
24165 / Phosphatidylinositol 3-kinase, catalytic, alpha polypeptide
nucleolar protein 3 (apoptosis repressor with CARD domain)
apoptosis, caspase activation inhibitor
ATG5 autophagy related 5 homolog (S. cerevisiae)
deoxyribonuclease II alpha
serine/threonine kinase 17b
voltage-dependent anion channel 1
v-akt murine thymoma viral oncogene homolog 1
ras homolog gene family, member A
adenosine deaminase / 1.27582
-1.21092
-1.21714
-1.22236
-1.22722
-1.23386
-1.24773
-1.24953
-1.23603
-1.22828 / 0.0018
0.0479
0.0003
0.0117
0.0353
0.0202
0.0310
0.0339
0.0240
0.0012
3. Cell cycle
Katna1
9-Sep
Ccndbp1
RGD1561797 / 292464
83788
362201
499655 / katanin p60 (ATPase-containing) subunit A1
septin 9
cyclin D-type binding-protein 1
RGD1561797 / -1.21188
-1.21834
-1.22470
-1.25161 / 0.0202
0.0353
0.0346
0.0288
4. Transcription
Jmjd1c
Etv1
Nr4a3
Gtf3a
Tfam
Anp32a
Usf1 / 171120
362733
58853
246299
83474
25379
83586 / jumonji domain containing 1C
ets variant 1
nuclear receptor subfamily 4, group A, member 3
general transcription factor III A
transcription factor A, mitochondrial
acidic (leucine-rich) nuclear phosphoprotein 32 family, member A
upstream transcription factor 1 / 1.31715
1.22634
1.20120
-1.20912
-1.22279
-1.23845
-1.33396 / 0.0333
0.0127
0.0192
0.0235
0.0002
0.0213
0.0008
5. Translation
Eif2b2
Mrpl10
Tufm / 84005
691075
293481 / eukaryotic translation initiation factor 2B, subunit 2 beta
mitochondrial ribosomal protein L10
Tu translation elongation factor, mitochondrial / -1.21311
-1.22841
-1.41427 / 0.0029
0.0152
0.0468
6. Biosynthetic process
Coasy
Mtfmt
Glt25d1
Coq5 / 287711
315763
290637
304542 / Coenzyme A synthase
mitochondrial methionyl-tRNA formyltransferase
glycosyltransferase 25 domain containing 1
coenzyme Q5 homolog, methyltransferase (S. cerevisiae) / -1.21595
-1.21274
-1.26379
-1.42783 / 0.0089
0.0110
0.0309
0.0310
7. Metabolic process
1) Lipids metabolic process
Gde1
Asah1
Echs1
P76 / 60418
84431
140547
246120 / glycerophosphodiester phosphodiesterase 1
N-acylsphingosine amidohydrolase (acid ceramidase) 1
enoyl Coenzyme A hydratase, short chain, 1, mitochondrial
mannose-6-phosphate protein p76 / -1.20321
-1.22573
-1.25843
-1.27333 / 0.0119
0.0270
0.0106
0.0332
2) Carbohydrate metabolic process
Phkg2
Cs
Nans / 140671
170587
298071 / phosphorylase kinase, gamma 2 (testis)
citrate synthase
N-acetylneuraminic acid synthase / -1.20829
-1.23533
-1.26492 / 0.0418
0.0370
0.0316
3) Protein and amino acid metabolic process
Cct5
Ivd / 294864
24513 / chaperonin containing Tcp1, subunit 5 (epsilon)
isovaleryl coenzyme A dehydrogenase / -1.22252
-1.21544 / 0.0128
0.0209
4) Energy metabolism and respiratory chain
Coq6
Atp6v1b2 / 299195
117596 / coenzyme Q6 homolog (yeast)
ATPase, H transporting, lysosomal V1 subunit B2 / -1.21832
-1.24512 / 0.0382
0.0109
5) Others metabolic process
Adh5
Dhrsx
Dhrs7b
Ephx1
Rnaseh2a / 29646
288525
287380
25315
364974 / alcohol dehydrogenase 5
dehydrogenase/reductase (SDR family) X-linked
dehydrogenase/reductase (SDR family) member 7B
epoxide hydrolase 1, microsomal
ribonuclease H2, subunit A / -1.21014
-1.22539
-1.23647
-1.27052
-1.24536 / 0.0241
0.0087
0.0231
0.0430
0.0204
8. Protein or nucleic acid binding
1) Protein binding
Mpdz
Cfh
Matr3
Thap7
Rragc
Cops4
Srprb
Lrrc59
Rhog
Gabarapl1
Ubac1
Gfer
Fam136a
RGD1307682
Coro1b
Tpm4
Mll5
RGD1562952
Klhl9
Dnajb1
Dhps
Ril
Eif3s6ip
Dstn
LOC684352
Cdc42ep2 / 29365
155012
29150
287944
298514
360915
300965
287633
308875
689161
362087
27100
297415
300675
29474
24852
311968
365661
313348
361384
288923
24915
300069
502674
684352
309175 / multiple PDZ domain protein
complement factor H
matrin 3
THAP domain containing 7
Ras-related GTP binding C
COP9 constitutive photomorphogenic homolog subunit 4
Signal recognition particle receptor, B subunit
leucine rich repeat containing 59
ras homolog gene family, member G (rho G)
GABA(A) receptor-associated protein like 1
UBA domain containing 1
growth factor, augmenter of liver regeneration
family with sequence similarity 136, member A
similar to hypothetical protein FLJ21827
coronin, actin-binding protein, 1B
tropomyosin 4
myeloid/lymphoid or mixed-lineage leukemia 5
similar to Erbb2 interacting protein isoform 2
kelch-like 9 (Drosophila)
DnaJ (Hsp40) homolog, subfamily B, member 1
deoxyhypusine synthase
reversion induced LIM gene
eukaryotic translation initiation factor 3, subunit 6 interacting protein
destrin
similar to twinfilin-like protein
CDC42 effector protein (Rho GTPase binding) 2 / 1.22511
1.24559
1.22033
-1.23198
-1.26466
-1.30890
-1.22864
-1.25881
-1.21151
-1.27937
-1.20454
-1.21689
-1.22541
-1.28375
-1.21581
-1.24755
1.26747
1.23813
1.21246
-1.32035
-1.32846
-1.21502
-1.27402
-1.22475
-1.22751
-1.20923 / 0.0131
0.0425
0.0230
0.0430
0.0221
0.0179
0.0230
0.0082
0.0142
0.0107
0.0129
0.0148
0.0003
0.0481
0.0130
0.0100
0.0246
0.0185
0.0417
0.0302
0.0053
0.0382
0.0094
0.0268
0.0283
0.0004
2) Nucleic acid binding
Larp5
Znf771
Eepd1 / 307070
308992
315500 / La ribonucleoprotein domain family, member 5
zinc finger protein 771
endonuclease/exonuclease/phosphatase family domain containing 1 / 1.26996
-1.30312
-1.24898 / 0.0014
0.0235
0.0103
9. Protein transport
Sil1
Vps16
Timm22
Tmed2
Tmed9
Ykt6
Arf1 / 291673
296159
79463
65165
361207
64351
64310 / SIL1 homolog, endoplasmic reticulum chaperone (S. cerevisiae)
vacuolar protein sorting 16 homolog (S. cerevisiae)
translocase of inner mitochondrial membrane 22 homolog (yeast)
transmembrane emp24 domain trafficking protein 2
transmembrane emp24 protein transport domain containing 9
YKT6 v-SNARE homolog (S. cerevisiae)
ADP-ribosylation factor 1 / -1.20459
-1.22628
-1.24058
-1.25862
-1.28757
-1.28744
-1.30577 / 0.0051
0.0458
0.0037
0.0100
0.0339
0.0363
0.0351
10. Proteolysis
Pmpcb
Amz2
C2 / 64198
360650
24231 / peptidase (mitochondrial processing) beta
archaelysin family metallopeptidase 2
complement component 2 / -1.21271
-1.22990
-1.23499 / 0.0229
0.0471
0.0385
11.Others
1) Known function
P2ry2
Yipf3
Rps6ka3
Alg3
Ppapdc3
Creld1
Ndufs2
Lgals8
Mpst
Slc35b4 / 29597
301245
501560
287983
296635
312638
289218
116641
192172
296969 / purinergic receptor P2Y, G-protein coupled 2
Yip1 domain family, member 3
ribosomal protein S6 kinase polypeptide 3
asparagine-linked glycosylation 3
phosphatidic acid phosphatase type 2 domain containing 3
cysteine-rich with EGF-like domains 1
NADH dehydrogenase (ubiquinone) Fe-S protein 2
lectin, galactoside-binding, soluble, 8
mercaptopyruvate sulfurtransferase
solute carrier family 35, member B4 / -1.23881
-1.32714
1.21593
-1.21214
-1.22126
-1.23218
-1.23313
-1.21059
-1.21147
-1.21424 / 0.0300
0.0484
0.0448
0.0478
0.0242
0.0151
0.0006
0.0080
0.0209
0.0324
2) Unknown function
Kab
Pcdh19
Mmp17
RGD1359310
Tnfaip2
RGD1559482
Cops7a
LOC683512
Sh3bp5l
Tmem86a
rCG_22919
Ccdc22
Dscr3
RGD620382
Ccdc51
LOC619574
Tmem35
Tmem106a
Tmem120a
C1qtnf7 / 171457
317183
288626
300240
299339
498022
312710
683512
690898
308602
100125364
317381
360703
171047
316008
619574
308134
287722
288591
305423 / KARP-1 binding protein 1
protocadherin 19
matrix metallopeptidase 17
similar to RIKEN cDNA 9430023L20
tumor necrosis factor, alpha-induced protein 2
similar to immunoglobulin superfamily, member 7
COP9 constitutive photomorphogenic homolog subunit 7A
similar to Basic FGF-repressed Zic-binding protein (mbFZb)
SH3 binding domain protein 5 like
transmembrane protein 86A
hypothetical protein LOC100125364
coiled-coil domain containing 22
Down syndrome critical region gene 3
Nucleoside 2-deoxyribosyltransferase domain containing protein
coiled-coil domain containing 51
hypothetical protein LOC619574
transmembrane protein 35
transmembrane protein 106A
transmembrane protein 120A
C1q and tumor necrosis factor related protein 7 / 1.25276
1.23382
-1.20701
-1.21887
-1.22355
-1.23486
-1.24624
-1.24918
-1.24747
-1.21032
-1.21549
-1.20383
-1.22164
-1.33534
-1.20460
-1.20676
-1.22216
-1.22272
-1.34952
-1.22536 / 0.0343
0.0311
0.0292
0.0090
0.0271
0.0368
0.0464
0.0245
0.0058
0.0117
0.0049
0.0223
0.0067
0.0308
0.0255
0.0223
0.0340
0.0216
0.0140
0.0374