| Literature DB >> 23304210 |
X G Zhang1, H Zhang, R Tan, J C Peng, X L Liang, Q Liu, M Q Wang, X P Yu.
Abstract
We aimed to investigate the mechanism of shaking as a prenatal stressor impacting the development of the offspring and Chinese medicines correcting the alterations. Pregnant rats were randomized into earthquake simulation group (ESG), herbal group (HG) which received herbal supplements in feed after shaking, and control group (CG). Findings revealed body weight and open field test (OFT) score of ESG offspring were statistically inferior to the CG and HG offspring. The corticosterone levels of ESG were higher than those of CG but not than HG. The dopamine level of ESG was slightly lower than that of the CG and of HG was higher than that of ESG. The 5-HT of ESG was higher than CG and HG. The growth hormone level of the ESG was significantly lower than ESG but not than CG. Gene expression profile showed 81 genes upregulated and 39 genes downregulated in ESG versus CG, and 60 genes upregulated and 28 genes downregulated in ESG versus HG. Eighty-four genes were found differentially expressed in ESG versus CG comparison and were normalized in ESG versus HG. We conclude that maternal shaking negatively affected physical and nervous system development, with specific alterations in neurohormones and gene expression. Chinese herbal medicine reduced these negative outcomes.Entities:
Year: 2012 PMID: 23304210 PMCID: PMC3523342 DOI: 10.1155/2012/670362
Source DB: PubMed Journal: Evid Based Complement Alternat Med ISSN: 1741-427X Impact factor: 2.629
QC of RNA extraction and slides experiment (A sample is qualified only when 2100 RIN ≥ 7.0 and 28S/18S ≥ 0.7).
| Group | QC of RNA | QC of slides | |||||||
|---|---|---|---|---|---|---|---|---|---|
| Con. ( | Vol. ( | Total ( | A260/A280 | 2100 Result | Result | CV (%)* | Detection rate (%) | ||
| RIN | 28S/18S | ||||||||
| ESG | 0.168 | 50 | 8.41 | 1.88 | 9.4 | 1.7 | Qualified | 3.91 | 69.50 |
| 1.366 | 30 | 40.98 | 1.93 | 9.5 | 1.8 | Qualified | 4.85 | 62.96 | |
| 0.246 | 50 | 12.29 | 1.90 | 9.4 | 1.7 | Qualified | 6.70 | 72.13 | |
| HG | 0.134 | 50 | 6.69 | 1.81 | 9.4 | 1.8 | Qualified | 4.76 | 70.40 |
| 0.138 | 50 | 6.92 | 1.82 | 9.4 | 1.8 | Qualified | 4.90 | 72.30 | |
| 0.372 | 50 | 18.58 | 1.86 | 9.5 | 1.6 | Qualified | 4.89 | 69.43 | |
| CG | 0.185 | 50 | 9.27 | 1.91 | 9.4 | 1.7 | Qualified | 6.33 | 61.09 |
| 0.595 | 50 | 29.75 | 1.93 | 9.4 | 1.7 | Qualified | 5.70 | 70.68 | |
| 0.355 | 25 | 8.87 | 1.85 | 9.3 | 1.6 | Qualified | 4.39 | 65.52 | |
*CV = SD/Mean × 100%.
Primers and product length of the four targeted genes.
| No. | Gene symbol | Forward primer | Reverse primer | Product |
|---|---|---|---|---|
| 1 | *ACTB | GCGTCCACCCGCGAGTACAA | ACATGCCGGAGCCGTTGTCG | 118 |
| 2 | Irf7 | TGGCAGATGGAAGCTACC | GGCTATACAGGAACACGC | 154 |
| 3 | Ninj2 | CCACCACCTTGGTCTTCATA | AGGCTGAAGTGGCTTTAG | 152 |
| 4 | Isca1 | CCCGTTGCATCTTTACCAC | GTCTAAGCAAACCGCATGAA | 151 |
| 5 | Plxnc1 | TGACCACTGCCACTTGAT | CTGAAGAGTTTCTCAAGCAC | 159 |
*refers to internal control gene.
Figure 1Mean plot of body weight. According to the ANOVA for Repeated Measurement, the body weight of ESG offspring were statistically all inferior to the CG offspring despite in Day 10 (P < 0.05). The body weight HG offspring were statistically superior to the ESG offspring despite in Day 5 (P < 0.05); The body weight HG in Day 15, Day 20 and Day 25 were statistically superior to the CG (P < 0.05).
Figure 2Box plot of OFT in the comparison between CG, ESG, and HG. ESG showed less scores than CG (P < 0.05) and HG (P < 0.05).
Figure 3ELISA outcomes of corticosterone, dopamine, 5-HT, and growth hormone. (a) ANOVA test for the corticosterone showed P = 0.027 in CG versus ESG, P = 0.491 in CG versus HG, and P = 0.111 in ESG versus HG. (b) ANOVA test for the dopamine showed P = 0.065 in CG versus ESG, P = 0.805 in CG versus HG, and P = 0.039 in ESG versus HG. (c) ANOVA test for 5-HT showed P = 0.000 in CG versus ESG, P = 0.004 in CG versus HG, and P = 0.013 in ESG versus HG. (d) ANOVA test for the growth hormone showed P = 0.135 in CG versus ESG, P = 0.034 in CG versus HG, and P = 0.001 in ESG versus HG.
Differentially expressed genes in ESG versus CG, among which 39 genes were upregulated and 81 genes downregulated.
| Gene ID |
| Fold change | Gene symbol | Regulation |
|---|---|---|---|---|
| 63847 | 0.007006 | 0.096204 | Fxyd6 | Downregulated |
| 498145 | 0.003225 | 0.17368 | LOC498145 | Downregulated |
| 316628 | 0.004414 | 0.274831 | Asb1 | Downregulated |
| 360547 | 0.005836 | 0.320844 | Sat2 | Downregulated |
| 301245 | 0.007067 | 0.331729 | Yipf3 | Downregulated |
| 293023 | 0.009502 | 0.335662 | Klhl25 | Downregulated |
| 288240 | 0.002174 | 0.344925 | Hlcs | Downregulated |
| 293180 | 0.007695 | 0.352823 | Micalcl | Downregulated |
| 316426 | 0.003961 | 0.363248 | Spats2l | Downregulated |
| 293624 | 0.008043 | 0.364195 | Irf7 | Downregulated |
| 683788 | 0.007907 | 0.382175 | LOC683788 | Downregulated |
| 293156 | 0.009012 | 0.413953 | Lrtomt | Downregulated |
| 25646 | 0.004102 | 0.429726 | Otx1 | Downregulated |
| 290232 | 0.009311 | 0.430944 | Tinf2 | Downregulated |
| 498353 | 0.002896 | 0.440115 | Scfd2 | Downregulated |
| 362873 | 0.006203 | 0.440433 | Plxnc1 | Downregulated |
| 309415 | 0.009479 | 0.458925 | Fam189a2 | Downregulated |
| 113894 | 0.007725 | 0.463149 | Sqstm1 | Downregulated |
| 303538 | 0.003261 | 0.465171 | Dhx58 | Downregulated |
| 406196 | 0.001118 | 0.467157 | Hcr | Downregulated |
| 313917 | 0.005676 | 0.482298 | Abhd1 | Downregulated |
| 292811 | 0.009904 | 0.48439 | Ccdc123 | Downregulated |
| 290985 | 0.007918 | 0.491881 | Isca1 | Downregulated |
| 405152 | 0.008771 | 0.516648 | Olr1192 | Downregulated |
| 171355 | 0.005274 | 0.519609 | Pou4f2 | Downregulated |
| 362943 | 0.000172 | 0.526926 | Adck5 | Downregulated |
| 309161 | 0.001612 | 0.543788 | Ccdc85b | Downregulated |
| 361327 | 0.003693 | 0.596748 | Prr16 | Downregulated |
| 24640 | 0.008865 | 0.602226 | Pfkfb2 | Downregulated |
| 619573 | 0.006811 | 0.603084 | Fam104a | Downregulated |
| 116725 | 0.007447 | 0.653258 | Ube2n | Downregulated |
| 304342 | 0.005141 | 0.662423 | Zscan21 | Downregulated |
| 192252 | 0.009069 | 0.671766 | Dctpp1 | Downregulated |
| 114205 | 0.00295 | 0.677239 | Crcp | Downregulated |
| 311430 | 0.007769 | 0.689602 | Mavs | Downregulated |
| 287840 | 0.003671 | 0.716317 | Fam100b | Downregulated |
| 297109 | 0.006823 | 0.764608 | MGC95152 | Downregulated |
| 295037 | 0.000491 | 0.788096 | Mgst2 | Downregulated |
| 100360990 | 0.007759 | 0.815928 | LOC100360990 | Downregulated |
| 501083 | 0.00564 | 1.179002 | Pdcd6ip | Upregulated |
| 299195 | 0.000513 | 1.189394 | Coq6 | Upregulated |
| 81716 | 0.007768 | 1.20684 | Ggcx | Upregulated |
| 315023 | 0.008157 | 1.265746 | Slc25a32 | Upregulated |
| 296753 | 0.009238 | 1.284846 | Srpk2 | Upregulated |
| 299147 | 0.005455 | 1.304917 | Ppp2r5e | Upregulated |
| 361932 | 0.009554 | 1.307515 | RGD1561393 | Upregulated |
| 288259 | 0.009614 | 1.31293 | Gart | Upregulated |
| 289522 | 0.002341 | 1.325268 | Cox18 | Upregulated |
| 50688 | 0.002132 | 1.334825 | Cacnb1 | Upregulated |
| 363171 | 0.000593 | 1.337206 | Tmem42 | Upregulated |
| 114215 | 0.005997 | 1.352079 | Insl3 | Upregulated |
| 315771 | 0.008317 | 1.369011 | Herc1 | Upregulated |
| 360389 | 0.009442 | 1.375028 | Zfp422 | Upregulated |
| 305923 | 0.008185 | 1.393988 | Zdhhc20 | Upregulated |
| 24803 | 0.005163 | 1.399617 | Vamp2 | Upregulated |
| 363210 | 0.001697 | 1.411325 | Phf3 | Upregulated |
| 50561 | 0.001722 | 1.425023 | Resp18 | Upregulated |
| 362367 | 0.005441 | 1.43527 | Znrf2 | Upregulated |
| 170841 | 0.009557 | 1.458549 | Mutyh | Upregulated |
| 81678 | 0.003588 | 1.464706 | Itpr2 | Upregulated |
| 502886 | 0.009395 | 1.466283 | Foxj2 | Upregulated |
| 360868 | 0.009274 | 1.471063 | Sft2d2 | Upregulated |
| 313757 | 0.005281 | 1.485264 | RGD1565591 | Upregulated |
| 361109 | 0.000669 | 1.486251 | Dcp1a | Upregulated |
| 192210 | 0.008713 | 1.487999 | Dnajc21 | Upregulated |
| 25262 | 0.008127 | 1.49478 | Itpr1 | Upregulated |
| 311112 | 0.00906 | 1.533447 | Fastkd1 | Upregulated |
| 64086 | 0.004012 | 1.55121 | Csnk1g1 | Upregulated |
| 366693 | 0.007515 | 1.567923 | Rbm25 | Upregulated |
| 690961 | 0.006894 | 1.577038 | Cog2 | Upregulated |
| 292148 | 0.004257 | 1.589999 | Eif3a | Upregulated |
| 691918 | 0.002531 | 1.596744 | LOC691918 | Upregulated |
| 362317 | 0.001503 | 1.599092 | Krit1 | Upregulated |
| 54323 | 0.001154 | 1.610286 | Arc | Upregulated |
| 304813 | 0.005676 | 1.614358 | Ppp1r12b | Upregulated |
| 58983 | 0.00216 | 1.617294 | Rabggta | Upregulated |
| 361944 | 0.004739 | 1.617335 | Elf2 | Upregulated |
| 314862 | 0.000215 | 1.618023 | Dyrk2 | Upregulated |
| 29642 | 0.003006 | 1.62079 | Slc38a2 | Upregulated |
| 291409 | 0.00357 | 1.622726 | Zfp236 | Upregulated |
| 246282 | 0.001061 | 1.623318 | Zfp91 | Upregulated |
| 362132 | 0.00226 | 1.626565 | Epc2 | Upregulated |
| 303963 | 0.002236 | 1.631518 | Dzip3 | Upregulated |
| 116670 | 0.006773 | 1.634179 | Ppp1r12a | Upregulated |
| 302670 | 0.004529 | 1.63737 | Zrsr2 | Upregulated |
| 360993 | 0.006601 | 1.637448 | Smek2 | Upregulated |
| 59319 | 0.001208 | 1.6438 | Nyw1 | Upregulated |
| 287249 | 0.009286 | 1.659325 | Cnot6 | Upregulated |
| 362132 | 0.007917 | 1.663529 | Epc2 | Upregulated |
| 303511 | 0.004368 | 1.665157 | Ikzf3 | Upregulated |
| 363210 | 0.008478 | 1.665263 | Phf3 | Upregulated |
| 362096 | 0.00268 | 1.668933 | Setx | Upregulated |
| 316583 | 0.001117 | 1.700923 | B3gnt7 | Upregulated |
| 362817 | 0.008175 | 1.701909 | Cdk2 | Upregulated |
| 304157 | 0.009185 | 1.708222 | Nrip1 | Upregulated |
| 314169 | 0.009008 | 1.729076 | Fam179b | Upregulated |
| 303919 | 0.007784 | 1.731828 | Lrrc58 | Upregulated |
| 309523 | 0.005447 | 1.734164 | Kif20b | Upregulated |
| 291773 | 0.003136 | 1.741424 | RGD1562997 | Upregulated |
| 314423 | 0.003545 | 1.743689 | Bcl11b | Upregulated |
| 362622 | 0.007916 | 1.756522 | Ccdc21 | Upregulated |
| 497198 | 0.005781 | 1.770803 | Impact | Upregulated |
| 315804 | 0.00029 | 1.773739 | Rfx7 | Upregulated |
| 363287 | 0.002339 | 1.775948 | Hdac4 | Upregulated |
| 361688 | 0.00606 | 1.778637 | Suv420h1 | Upregulated |
| 363555 | 0.002239 | 1.787221 | Wfikkn1 | Upregulated |
| 304809 | 0.001337 | 1.791911 | Kdm5b | Upregulated |
| 498803 | 0.003675 | 1.797804 | Otud1 | Upregulated |
| 64624 | 0.005484 | 1.803225 | Cul5 | Upregulated |
| 304817 | 0.00381 | 1.807047 | Ipo9 | Upregulated |
| 54311 | 0.008729 | 1.82334 | Timm17a | Upregulated |
| 25486 | 0.008651 | 1.8782 | Myo9b | Upregulated |
| 302612 | 0.006615 | 1.978189 | Tspyl2 | Upregulated |
| 293765 | 0.003013 | 2.076238 | Olr327 | Upregulated |
| 171347 | 0.007854 | 2.324322 | Mat2a | Upregulated |
| 685074 | 0.008629 | 2.417108 | LOC685074 | Upregulated |
| 498211 | 0.007458 | 2.449546 | RGD1560523 | Upregulated |
| 690043 | 0.004624 | 2.470614 | Rnf168 | Upregulated |
| 171347 | 0.00179 | 2.47901 | Mat2a | Upregulated |
| 363083 | 0.007379 | 2.521284 | Fbxl22 | Upregulated |
Figure 4Heat map of the differently expressed genes. R2_1_NS, R2_2_NS, and R2_3_NS refer to ESG and R4_1_NS, R4_2_NS, R4_3_NS to CG.
Significant GO annotation of the 120 differentially expressed genes and the genes involved (P < 0.05).
| GO Id | Name | Symbol | Hits | Total | Percent | Enrichment test |
|---|---|---|---|---|---|---|
| GO: 0016874 | Ligase activity | Ube2n, Hlcs | ||||
| Gart, Herc1, | 7 | 308 | 2.27% | 0.0083 | ||
| Cul5, Rnf168, Ggcx | ||||||
|
| ||||||
| GO: 0019222 | Regulation of metabolic process | Sqstm1, Insl3, Ube2n, Pou4f2, | ||||
| Otx1, Cnot6, Tinf2, | ||||||
| RGD1562997, Irf7, | ||||||
| Tspyl2, Nrip1, | 28 | 2415 | 1.16% | 0.0089 | ||
| Zscan21, Jarid1b, Bcl11b, Dyrk2, | ||||||
| Mll1, Rfx7, Zfp422, Smek2, Suv420h1, Elf2, Cdk2, Hdac4, Impact, | ||||||
| Foxj2, Rasd1, Rnf168, Pfn2 | ||||||
|
| ||||||
| GO: 0009893 | Positive regulation of metabolic process | Sqstm1, Insl3, Ube2n, | ||||
| Pou4f2, Tinf2, | ||||||
| Nrip1, Zscan21, Bcl11b | 13 | 846 | 1.54% | 0.0098 | ||
| Dyrk2, Mll1, Cdk2 | ||||||
| Hdac4, Rnf168 | ||||||
|
| ||||||
| GO: 0022607 | Cellular component assembly | Sqstm1, Xtp3tpa | ||||
| Vamp2, Cox18, Tinf2, Eif3s10, RGD1562997 | 12 | 786 | 1.53% | 0.0135 | ||
| Srpk2, Mll1, Enth, Pfn2 | ||||||
|
| ||||||
| GO: 0043227 | Membrane-bounded organelle | Sqstm1, Crcp, Ube2n, Mutyh, Pou4f2, Vamp2 | ||||
| Itpr1, Otx1, Cnot6 | ||||||
| Hlcs, Cox18, Tinf2 | ||||||
| Isca1, Eif3s10 | ||||||
| RGD1562997 | ||||||
| Irf7, Srpk2, Ikzf3 | ||||||
| Ppp2r5e, Yipf3 | ||||||
| Tspyl2, Zrsr2, Nrip1 | ||||||
| Zscan21, Kif20b | ||||||
| Visa, RGD1565591 | 55 | 5982 | 0.92% | 0.025 | ||
| Bcl11b, Dyrk2 | ||||||
| Slc25a32, Mll1, Enth | ||||||
| B3gnt7, Zfp422, Setx | ||||||
| Suv420h1, Elf2, Phf3 | ||||||
| Cdk2, Adck5, Hdac4 Hcr, LOC498145 | ||||||
| Pdcd6ip, Foxj2, Rasd1, Resp18, Cul5 | ||||||
| Cacnb1,Timm17a, | ||||||
| Arc, Rnf168, Cog2, | ||||||
| Itpr2, Ggcx | ||||||
|
| ||||||
| GO: 0014854 | Response to inactivity | Hdac4 | 1 | 3 | 33.33% | 0.0288 |
|
| ||||||
| GO: 0009058 | Biosynthetic process | Crcp, Insl3,Ube2n | ||||
| Mat2a, Pou4f2, Otx1 | ||||||
| Cnot6, Gart, Tinf2 | ||||||
| Isca1, RGD1562997 | ||||||
| Eif3s10, Irf7, Coq6 | ||||||
| Tspyl2, Nrip1, Mll1 | 34 | 3379 | 1.01% | 0.0291 | ||
| Zscan21, Jarid1b | ||||||
| Bcl11b, Dyrk2, Rfx7 | ||||||
| B3gnt7, Zfp422, Elf2 | ||||||
| Suv420h1, Cdk2, Phf3 | ||||||
| Hdac4, Impact, Foxj2 | ||||||
| Rabggta, Rasd1 | ||||||
|
| ||||||
| GO: 0044085 | Cellular component biogenesis | Sqstm1, Xtp3tpa, | ||||
| Vamp2, Cox18, Tinf2 | ||||||
| RGD1562997, Eif3s10 | 12 | 883 | 1.36% | 0.0299 | ||
| Srpk2, Mll1, Enth, Pfn2 | ||||||
|
| ||||||
| GO: 0014874 | Response to stimulus involved in regulation of muscle adaptation | Hdac4 | 1 | 4 | 25.00% | 0.0359 |
|
| ||||||
| GO: 0043233 | Organelle lumen | Sqstm1, Mutyh, Itpr1 | ||||
| Tinf2, RGD1562997 | ||||||
| Srpk2, Tspyl2, Zrsr2 | 16 | 1360 | 1.18% | 0.0416 | ||
| Nrip1, Kif20b, Mll1 | ||||||
| Zfp422, Setx, Cdk2 | ||||||
| Hdac4, Resp18 | ||||||
|
| ||||||
| GO: 0051716 | Cellular response to stimulus | Ube2n, Mutyh, Dyrk2 | ||||
| Mll1, Setx, Cdk2, | 8 | 528 | 1.52% | 0.0422 | ||
| Pdcd6ip, Rnf168 | ||||||
|
| ||||||
| GO: 0016740 | Transferase activity | Crcp, Mat2a, Pfkfb2 | ||||
| Gart, Mgst2, Srpk2 | ||||||
| RGD1304822, Dyrk2 | 18 | 1612 | 1.12% | 0.0483 | ||
| Fastkd1, Mll1, B3gnt7 | ||||||
| Suv420h1, Cdk2, Fgfr1l, RGD1560523 | ||||||
| Rabggta, Csnk1g1 | ||||||
|
| ||||||
| GO: 0031974 | Membrane enclosed lumen | Sqstm1, Mutyh, Itpr1 | ||||
| Tinf2, RGD1562997 | ||||||
| Srpk2, Tspyl2, Zrsr2 | ||||||
| Nrip1, Kif20b, Mll1 | 16 | 1392 | 1.15% | 0.0495 | ||
| Zfp422, Setx, Cdk2, | ||||||
| Hdac4, Resp18 | ||||||
|
| ||||||
| GO: 0031077 | Postembryonic camera-type eye development | Bcl11b | 1 | 6 | 16.67% | 0.0499 |
KEGG Pathway annotation of the 120 differentially expressed genes (P < 0.05, q < 0.05) (↓ refers downregulation, ↑ refers upregulation).
| Name | Symbol | Total | Percent | Enrichment |
|
|---|---|---|---|---|---|
| Oocyte meiosis | Itpr1↑ Ppp2r5e↑ | 116 | 0.0345 | 0.0008 | 0.0048 |
| Cdk2↑ | |||||
| Vascular smooth muscle contraction | Ppp1r12a↑ | 128 | 0.0313 | 0.0011 | 0.0048 |
| Itpr1↑ | |||||
| Ppp1r12b↑ | |||||
| RIG-I-like receptor signaling pathway | Irf7↓ Dhx58↓ | 64 | 0.0469 | 0.0016 | 0.0048 |
| Mavs↓ | |||||
| Long-term potentiation | Ppp1r12a↑ Itpr1↑ | 72 | 0.0417 | 0.0022 | 0.0049 |
| Itpr2↑ | |||||
| Ubiquitin mediated proteolysis | Ube2n↓ Herc1↑ | 132 | 0.0227 | 0.0111 | 0.0176 |
| Cul5↑ | |||||
| Cytosolic DNA-sensing pathway | Irf7↓ Mavs↓ | 49 | 0.0408 | 0.0131 | 0.0176 |
| Biotin metabolism | Hlcs↓ | 3 | 0.3333 | 0.0135 | 0.0176 |
| RNA degradation | Cnot6↑ Dcp1a↑ | 61 | 0.0328 | 0.0196 | 0.0223 |
| Long-term depression | Itpr1↑ Itpr2↑ | 69 | 0.029 | 0.0245 | 0.0245 |
| Ubiquinone and other terpenoid-quinone biosynthesis | Coq6↑ | 7 | 0.1429 | 0.0269 | 0.0245 |
| Phosphatidylinositol signaling system | Itpr2↑ Itpr1↑ | 77 | 0.026 | 0.0299 | 0.0247 |
| Gap junction | Itpr2↑ Itpr1↑ | 87 | 0.023 | 0.0371 | 0.0281 |
| GnRH signaling pathway | Itpr1↑ Itpr2↑ | 99 | 0.0202 | 0.0467 | 0.0326 |
Differentially expressed genes in ESG versus HG, among which 60 genes were upregulated and 28 genes downregulated.
| Gene ID |
| Fold change | Symbol | Remark |
|---|---|---|---|---|
| 287881 | 0.006042 | 0.220799 | Dysfip1 | Downregulated |
| 25405 | 0.004824 | 0.344631 | Ccng1 | Downregulated |
| 24237 | 0.003207 | 0.40894 | C6 | Downregulated |
| 313219 | 0.003811 | 0.410283 | Zfp189 | Downregulated |
| 287343 | 0.008194 | 0.499299 | Olr1454 | Downregulated |
| 293156 | 0.008272 | 0.508908 | Lrtomt | Downregulated |
| 405143 | 0.009972 | 0.5345 | Olr803 | Downregulated |
| 116724 | 0.000512 | 0.546672 | Epb4.1l3 | Downregulated |
| 313917 | 0.00383 | 0.578297 | Abhd1 | Downregulated |
| 83681 | 0.004251 | 0.581219 | Cish | Downregulated |
| 301346 | 0.007628 | 0.609505 | Sema4c | Downregulated |
| 315346 | 0.003519 | 0.619843 | Itga5 | Downregulated |
| 56825 | 0.009009 | 0.625224 | Cym | Downregulated |
| 690810 | 0.007066 | 0.637375 | Adat1 | Downregulated |
| 313982 | 0.009162 | 0.653927 | RGD1561890 | Downregulated |
| 363285 | 0.004745 | 0.660307 | Scly | Downregulated |
| 316090 | 0.003533 | 0.683347 | Fam198a | Downregulated |
| 24513 | 0.003494 | 0.687818 | Ivd | Downregulated |
| 303384 | 0.007792 | 0.703077 | Mmp28 | Downregulated |
| 246074 | 0.009445 | 0.718762 | Scd1 | Downregulated |
| 500011 | 0.008188 | 0.726294 | RGD1563091 | Downregulated |
| 362943 | 0.004839 | 0.735253 | Adck5 | Downregulated |
| 500420 | 0.008119 | 0.744282 | LOC500420 | Downregulated |
| 399489 | 0.006413 | 0.763541 | E2f1 | Downregulated |
| 311716 | 0.004912 | 0.77549 | Col20a1 | Downregulated |
| 113894 | 0.007846 | 0.78406 | Sqstm1 | Downregulated |
| 266609 | 0.005228 | 0.798742 | Bles03 | Downregulated |
| 246766 | 0.00514 | 0.821038 | Ggta1 | Downregulated |
| 288518 | 0.008613 | 1.136098 | RGD1311660 | Upregulated |
| 499430 | 0.008063 | 1.148146 | Lrrc20 | Upregulated |
| 317399 | 0.000156 | 1.156541 | Ddx21 | Upregulated |
| 306182 | 0.00808 | 1.160148 | Ipo5 | Upregulated |
| 301038 | 0.00729 | 1.178184 | Ubp1 | Upregulated |
| 310806 | 0.006399 | 1.178549 | Cdc14a | Upregulated |
| 287954 | 0.003091 | 1.181263 | Dgcr8 | Upregulated |
| 260321 | 0.008611 | 1.181875 | Fkbp4 | Upregulated |
| 305828 | 0.006609 | 1.182203 | Socs4 | Upregulated |
| 64161 | 0.005932 | 1.183779 | Pi4ka | Upregulated |
| 290679 | 0.009165 | 1.186593 | Ints10 | Upregulated |
| 298429 | 0.006198 | 1.188777 | Rad54l | Upregulated |
| 474154 | 0.005077 | 1.190852 | Rbm4b | Upregulated |
| 288717 | 0.006268 | 1.196619 | Srrd | Upregulated |
| 296312 | 0.004568 | 1.197256 | RGD1311066 | Upregulated |
| 312640 | 0.005739 | 1.198178 | Tmem111 | Upregulated |
| 83624 | 0.009311 | 1.200882 | Ppig | Upregulated |
| 288778 | 0.001749 | 1.22319 | Pa2g4 | Upregulated |
| 362851 | 0.004166 | 1.224723 | Cd320 | Upregulated |
| 308404 | 0.006579 | 1.227818 | Irf2bp1 | Upregulated |
| 363760 | 0.005704 | 1.237527 | Arl6 | Upregulated |
| 296076 | 0.007529 | 1.238081 | Srp14 | Upregulated |
| 291787 | 6.57 | 1.242186 | Rbbp8 | Upregulated |
| 500727 | 0.00344 | 1.246021 | Cdca4 | Upregulated |
| 306587 | 0.008906 | 1.255527 | Tcta | Upregulated |
| 29541 | 0.000917 | 1.259108 | Nthl1 | Upregulated |
| 360855 | 0.004605 | 1.26267 | Smg7 | Upregulated |
| 362317 | 0.008649 | 1.284527 | Krit1 | Upregulated |
| 313757 | 0.004801 | 1.294664 | RGD1565591 | Upregulated |
| 499370 | 0.009663 | 1.326682 | Itprip | Upregulated |
| 288259 | 0.009472 | 1.335197 | Gart | Upregulated |
| 29704 | 0.002213 | 1.349013 | Pacsin1 | Upregulated |
| 84472 | 0.006393 | 1.366251 | Ilf3 | Upregulated |
| 363210 | 0.006023 | 1.388566 | Phf3 | Upregulated |
| 680451 | 0.005563 | 1.419061 | Nrbp2 | Upregulated |
| 311112 | 0.001699 | 1.426768 | Fastkd1 | Upregulated |
| 54323 | 0.001608 | 1.4509 | Arc | Upregulated |
| 309136 | 0.006405 | 1.452428 | Oraov1 | Upregulated |
| 363169 | 0.005748 | 1.472567 | Toag1 | Upregulated |
| 29642 | 0.004937 | 1.475875 | Slc38a2 | Upregulated |
| 305461 | 0.004104 | 1.475879 | Fam53a | Upregulated |
| 304813 | 0.00934 | 1.481691 | Ppp1r12b | Upregulated |
| 680006 | 0.007932 | 1.484512 | Mad1l1 | Upregulated |
| 304474 | 0.001635 | 1.497221 | Pitpnm2 | Upregulated |
| 115768 | 0.009088 | 1.509009 | Zfp37 | Upregulated |
| 301513 | 0.001268 | 1.512431 | Rqcd1 | Upregulated |
| 363273 | 0.009331 | 1.521116 | Cops7b | Upregulated |
| 293511 | 0.008749 | 1.533752 | Znf688 | Upregulated |
| 245966 | 0.004372 | 1.544613 | Tmem150a | Upregulated |
| 291409 | 0.003844 | 1.552189 | Zfp236 | Upregulated |
| 84607 | 0.007931 | 1.552588 | Socs2 | Upregulated |
| 306344 | 0.007778 | 1.569477 | Arrdc2 | Upregulated |
| 309828 | 0.006302 | 1.584851 | Tspyl4 | Upregulated |
| 501095 | 0.009284 | 1.589281 | Rftn1 | Upregulated |
| 81531 | 0.008017 | 1.606129 | Pfn2 | Upregulated |
| 293152 | 0.007896 | 1.613085 | Art2b | Upregulated |
| 497040 | 0.006162 | 1.71037 | Prss36 | Upregulated |
| 171454 | 0.009816 | 1.850404 | Nacc1 | Upregulated |
| 363827 | 0.00216 | 1.948295 | LOC363827 | Upregulated |
| 364361 | 0.001905 | 4.479744 | RGD1563700 | Upregulated |
Figure 5Heat map of the differently expressed genes. R2_1_NS, R2_2_NS, and R2_3_NS refer to ESG and R3_1_NS, R3_2_NS, R3_3_NS to HG.
Significant GO Annotation of the 5 differentially expressed genes and the genes included (P < 0.05).
| GO ID | Name | Symbol | Hits | Total | Percent | Enrichment test |
|---|---|---|---|---|---|---|
| GO: 0031503 | Protein complex localization | Fkbp4 | 1 | 5 | 20.00% | 0.0309 |
| GO: 0022607 | Cellular component assembly | Sqstm1, Nacc1, Ivd, Fkbp4, Tspyl4, Itga5, Pfn2 | 8 | 786 | 1.02% | 0.0548 |
| GO: 0044085 | Cellular component biogenesis | Sqstm1, Nacc1, Ivd, Fkbp4, Tspyl4, Itga5, Pfn2 | 8 | 883 | 0.91% | 0.0926 |
| GO: 0010926 | Anatomical structure formation | Sqstm1, Nacc1, Ivd, Fkbp4, Ubp1, Tspyl4, Itga5, Pfn2 | 9 | 1049 | 0.86% | 0.0993 |
| GO: 0043233 | Organelle lumen | Sqstm1, Nacc1, Ivd, Fkbp4, Pa2g4, Ints10, Nthl1, Ddx21, E2f1, Rbm4b, Ppig | 11 | 1360 | 0.81% | 0.0994 |
KEGG Pathway annotation of the 120 differentially expressed genes (P < 0.05, q < 0.05) (↓ refers downregulation, ↑ refers upregulation).
| Name | Symbol | Total | Percent | Enrichment test |
|
|---|---|---|---|---|---|
| Cell cycle | Cdc14a↑ | 132 | 0.0227 | 0.0044 | 0.0067 |
| E2f1↓ | |||||
| Mad1l1↑ | |||||
| Jak-STAT signaling pathway | Socs4↑ | 149 | 0.0201 | 0.0062 | 0.0067 |
| Cish↓ | |||||
| Socs2↑ | |||||
| Type II diabetes mellitus | Socs4↑ | 53 | 0.0377 | 0.008 | 0.0067 |
| Socs2↑ | |||||
| One carbon pool by folate | Gart↑ | 17 | 0.0588 | 0.0429 | 0.0158 |
| Insulin signaling pathway | Socs4↑ | 140 | 0.0143 | 0.0471 | 0.0158 |
| Socs2↑ |
The 84 genes differently expressed in ESG and normalized in HG (the P value and fold change of ESG versus CG ).
| Gene ID |
| Fold change | Symbol | Description |
|---|---|---|---|---|
| 287443 | 0.0414 | 2.0120 | Acap1 | ArfGAP with coiled-coil, ankyrin repeat, and PH domains 1 |
| 316628 | 0.0044 | 0.2748 | Asb1 | Ankyrin repeat and SOCS box-containing 1 (Asb1), mRNA |
| 307970 | 0.0397 | 0.3289 | Atxn1l | PREDICTED: similar to Ataxin-1 (Spinocerebellar ataxia type 1 protein homolog) |
| 304127 | 0.0266 | 0.4310 | Bach1 | BTB and CNC homology 1, basic leucine zipper transcription factor 1 |
| 94342 | 0.0368 | 0.4621 | Bat3 | HLA-B-associated transcript 3, transcript variant 2, |
| 308588 | 0.0241 | 0.4679 | Car11 | Carbonic anhydrase-related XI protein |
| 81780 | 0.0349 | 2.6298 | Ccl5 | Chemokine (C-C motif) ligand 5 |
| 25405 | 0.0303 | 0.3845 | Ccng1 | Cyclin G1 |
| 362217 | 0.0393 | 0.4273 | Cenpb | PREDICTED: centromere protein B |
| 314004 | 0.0237 | 0.3330 | Cmpk2 | Cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial, nuclear gene encoding mitochondrial protein |
| 24273 | 0.0401 | 0.4750 | Cryaa | Crystallin, alpha A |
| 361729 | 0.0183 | 0.4488 | Cybasc3 | Cytochrome b, ascorbate dependent 3 |
| 308942 | 0.0369 | 0.3530 | Dennd5a | DENN/MADD domain containing 5A |
| 360583 | 0.0296 | 0.4192 | Dhrs11 | Dehydrogenase/reductase (SDR family) member 11 |
| 362293 | 0.0203 | 0.4955 | Dnajb6 | DnaJ (Hsp40) homolog, subfamily B, member 6 |
| 81655 | 0.0336 | 0.4654 | Dync1li2 | Dynein, cytoplasmic 1 light intermediate chain 2 |
| 59117 | 0.0343 | 0.3116 | Eif2c2 | Eukaryotic translation initiation factor 2C, 2 |
| 497983 | 0.0476 | 0.4848 | Fam117a | Family with sequence similarity 117, member A |
| 363083 | 0.0074 | 2.5213 | Fbxl22 | F-box and leucine-rich repeat protein 22 |
| 29292 | 0.0293 | 0.4455 | Ftl | Ferritin, light polypeptide |
| 54281 | 0.0281 | 0.3897 | Furin | Furin (paired basic amino acid cleaving enzyme) |
| 25172 | 0.0185 | 0.3991 | Gata1 | GATA binding protein 1 |
| 293267 | 0.0274 | 0.3516 | Hbe1 | Hemoglobin, epsilon 1 |
| 94164 | 0.0175 | 0.4161 | Hbg1 | Hemoglobin, gamma A |
| 498008 | 0.0335 | 2.2484 | Hexim1 | Hexamethylene bis-acetamide inducible 1 |
| 365895 | 0.0417 | 0.3894 | Hipk1 | Homeodomain interacting protein kinase 1 |
| 288240 | 0.0022 | 0.3449 | Hlcs | PREDICTED: holocarboxylase synthetase (biotin-(proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)) ligase) |
| 293624 | 0.0080 | 0.3642 | Irf7 | Interferon regulatory factor 7 |
| 290985 | 0.0079 | 0.4919 | Isca1 | Iron-sulfur cluster assembly 1 homolog (S. cerevisiae) |
| 298693 | 0.0462 | 0.3402 | Isg15 | ISG15 ubiquitin-like modifier |
| 25118 | 0.0351 | 2.9262 | Itga1 | Integrin, alpha 1 |
| 300317 | 0.0493 | 0.4873 | Kctd17 | Potassium channel tetramerisation domain containing 17 |
| 25110 | 0.0410 | 2.6060 | Klrd1 | Killer cell lectin-like receptor, subfamily D, member 1 |
| 245955 | 0.0120 | 0.4700 | Lgals3bp | Lectin, galactoside-binding, soluble, 3 binding protein |
| 25476 | 0.0214 | 0.4406 | Lgals9 | Lectin, galactoside-binding, soluble, 9 |
| 100365370 | 0.0172 | 0.4588 | LOC100365370 | PREDICTED: nuclear LIM interactor-interacting factor 2-like |
| 498145 | 0.0213 | 0.3006 | LOC498145 | Similar to RIKEN cDNA 2810453I06 |
| 679596 | 0.0155 | 0.4814 | LOC679596 | PREDICTED: similar to GABA(A) receptor-associated protein like 2 |
| 684112 | 0.0121 | 0.4067 | LOC684112 | PREDICTED: similar to KIAA0999 protein |
| 293156 | 0.0090 | 0.4140 | Lrtomt | Leucine rich transmembrane and 0-methyltransferase domain containing |
| 294241 | 0.0443 | 0.2072 | Ly6g6c | Lymphocyte antigen 6 complex, locus G6C |
| 117558 | 0.0498 | 0.3267 | Mylk2 | Myosin light chain kinase 2 |
| 85482 | 0.0360 | 0.4205 | Nbn | Nibrin |
| 366998 | 0.0309 | 0.4486 | Nfe2 | Nuclear factor, erythroid derived 2 |
| 59115 | 0.0355 | 0.3302 | Ninj2 | Ninjurin 2 |
| 245980 | 0.0238 | 0.4878 | Nr2f6 | Nuclear receptor subfamily 2, group F, member 6 |
| 287328 | 0.0292 | 0.4931 | Olr1439 | Olfactory receptor 1439 |
| 287520 | 0.0498 | 0.4482 | Olr1516 | Olfactory receptor 1516 |
| 366104 | 0.0175 | 0.4251 | Olr541 | Olfactory receptor 541 |
| 246294 | 0.0120 | 0.3491 | Optn | Optineurin |
| 362973 | 0.0467 | 0.4896 | Parvb | Parvin, beta |
| 24649 | 0.0147 | 0.3899 | Pim1 | Pim-1 oncogene |
| 64534 | 0.0423 | 2.1733 | Pim3 | Pim-3 oncogene |
| 301173 | 0.0478 | 0.3759 | Plcl2 | Phospholipase C-like 2 |
| 310674 | 0.0473 | 0.4134 | Plekho1 | Pleckstrin homology domain containing, family O member 1 |
| 362873 | 0.0062 | 0.4404 | Plxnc1 | Plexin C1 |
| 362248 | 0.0215 | 0.4759 | Procr | Protein C receptor, endothelial |
| 309381 | 0.0286 | 2.2397 | Pyroxd2 | Pyridine nucleotide-disulphide oxidoreductase domain 2 |
| 171452 | 0.0460 | 0.3652 | Rab3il1 | RAB3A interacting protein |
| 56820 | 0.0334 | 0.1273 | Ramp3 | Receptor (G protein-coupled) activity modifying protein 3 |
| 498659 | 0.0473 | 7.0377 | RatNP-3b | Defensin RatNP-3 precursor |
| 296408 | 0.0259 | 0.4348 | RGD1311378 | Similar to RIKEN cDNA 2010011I20 |
| 501644 | 0.0175 | 0.4259 | RGD1561055 | PREDICTED: similar to Ferritin light chain 2 (Ferritin L subunit 2) (Ferritin subunit LG) |
| 65190 | 0.0454 | 0.3257 | Rsad2 | Radical S-adenosyl methionine domain containing 2 |
| 24974 | 0.0165 | 0.4619 | RT1-A2 | RT1 class Ia, locus A2 (RT1-A2) |
| 414779 | 0.0105 | 0.4766 | RT1-CE2 | RT1 class I, locus CE2 (RT1-CE2) |
| 266758 | 0.0163 | 2.6183 | Sec11c | SEC11 homolog C (S. cerevisiae) |
| 313057 | 0.0446 | 0.4886 | Serinc2 | Serine incorporator 2 |
| 498546 | 0.0120 | 0.1863 | Serp2 | Stress-associated endoplasmic reticulum protein family member 2 |
| 360636 | 0.0484 | 0.4722 | Slc25a39 | Solute carrier family 25, member 39 (Slc25a39) |
| 192208 | 0.0472 | 0.3469 | Slc38a5 | Solute carrier family 38, member 5 (Slc38a5) |
| 300191 | 0.0457 | 0.4485 | Slc48a1 | Solute carrier family 48 (heme transporter), member 1 |
| 64630 | 0.0330 | 0.4620 | Snap23 | Synaptosomal-associated protein 23 |
| 314251 | 0.0353 | 0.4407 | Sptb | Spectrin, beta, erythrocytic |
| 113894 | 0.0230 | 0.4367 | Sqstm1 | Sequestosome 1, transcript variant 1, mRNA |
| 501146 | 0.0449 | 0.3749 | Stradb | STE20-related kinase adaptor beta |
| 24851 | 0.0449 | 0.3944 | Tpm1 | Tropomyosin 1, alpha |
| 303167 | 0.0390 | 0.3720 | Trim58 | Predicted: tripartite motif-containing 58 |
| 362087 | 0.0450 | 0.3958 | Ubac1 | UBA domain containing 1 |
| 295704 | 0.0234 | 0.3510 | Ube2l6 | Ubiquitin-conjugating enzyme E2L 6 |
| 310633 | 0.0316 | 0.3751 | Ubqln4 | Ubiquilin 4 |
| 289229 | 0.0240 | 0.3468 | Vangl2 | Vang-like 2 |
| 24874 | 0.0262 | 2.6865 | Vhl | Von Hippel-Lindau tumor suppressor |
| 298765 | 0.0209 | 2.4995 | Zfp36l2 | Zinc finger protein 36, C3H type-like 2 |
Figure 6RT-PCR validation of the selected four genes from gene expression profile chips, that is, Irf7, Ninj2, and Plxnc1, and Isca1. ΔΔCt < 0 indicates the target genes were hyperexpressed in ESG/HG comparing with CG while ΔΔCt > 0 indicates the target genes were hypoexpressed in ESG/HG comparing with CG. FC > 2 indicates the target genes were hyperexpressed in ESG/HG comparing with CG while FC < 0.5 indicates the target genes were hypoexpressed in ESG/HG comparing with CG.