黑猩猩和人类左脑成纤维细胞生长因子1（FGF1）不同分子网络和机制的功能预测
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摘要
在本文中,我们的目标是分别建立黑猩猩左脑和人类左脑的上下游激活和抑制网络。我们使用的芯片中,包含了12558个来自于15个黑猩猩左脑样本和14个人类左脑样本的基因。我们所使用的显著性表达基因标记,是通过使用微阵列的显著性差异分析方法而得到的。我们通过将数据进行log2的归一化处理,并运用聚类分析方法进行分析。首先,我们使用GRNInfer工具,构建了441个具有显著性高和低表达分子的整体网络；第二,我们从已构建的黑猩猩和人类左脑的整体网络中,确定了成纤维细胞生长因子1 (FGF1)的表达特性；第三,我们确定了黑猩猩和人类左脑的成纤维细胞生长因子1 (FGF1)的上下游网络；第四,我们从黑猩猩和人类左脑的成纤维细胞生长因子1 (FGF1)的上下游网络中进一步确认了分子的激活和抑制特性。我们使用的生物学分析方法已经得到了生物医学领域相关专家的承认,并给予了高度评价,所发表的论文分别刊登在SCI检索的国际杂志上,例如Cell Biochemistry and Biophysics (影响因子4.311), Journal of Cellular Biochemistry(影响因子3.121), Cell Proliferation (影响因子2.742),Cellular and Molecular Neurobiology (影响因子2.423)。
在本文中,我们通过GO数据库中的基因数据分析发现,分子FGF1的相关模块包括：细胞外区,细胞外基质,细胞外空间,蛋白结合,生长因子活性,肝素结合,血管生成,器官诱导,信号传导,发育,细胞增殖,成细胞生长因子受体信号通路,形态发生,细胞分化,肺发育,上皮细胞增殖的正调控。我们通过将黑猩猩的左脑和人类左脑进行比较,从而在黑猩猩的左脑中分别构建了低表达的成纤维细胞生长因子1 (FGF1)的DNA损伤介导的双链断裂重组修复,耦合了细胞分裂到端粒维持的抗凋亡网络和成纤维细胞生长因子1 (FGF1)的先天免疫驱动的转录耦合端粒维持的缩短导致细胞凋亡的调控网络。而成纤维细胞生长因子1 (FGF1)在人类左脑中,当基因表达改变最小倍数设为2倍时表现为高表达的特性。我们在人类左脑中分别构建了高表达的成纤维细胞生长因子1 (FGF1)的防御响应介导的迁移耦合绑定运输的信号到氧化代谢的诱导树突发育网络和高表达的成纤维细胞生长因子1 (FGF1)的DNA修复的迁移耦合到轴突扩建正调控转录抑制网络。我们的研究结果表明,在黑猩猩左脑中,上游激活网络：分子C10ORF10, CDC25B, LOH11CR2A, RAD50, SAPS2, STAMBP激活FGF1;而在下游的激活网络中,FGF1没有激活任何分子；上游抑制网络：AL049278, AL080232, CFHR1, CTBP1, DDX3Y, RNF2, RPP14, SARM1, TERF1_1抑制FGF1;而下游抑制网络没有相应的结果。在人类的左脑中,上游激活网络：分子CTRL, GPD1, LGALS3BP, MAP1B_3, PCDHGA8, PCSK6, PDIA2激活FGF1;而在下游的激活网络中,FGF1激活分子MGC15523, NUPR1, UBXD2;上游网络：DTNA, FOXN3_1, MAPT, NAIP, NR1D2_2, SLC25A46, SMG1抑制FGF1;而下游网络：FGF1抑制分子ISCA1, PSMA4, U79289。我们对成纤维细胞生长因子1 (FGF1)的研究对于神经退化性疾病的研究以及临床治疗具有重要作用,对于利用基因进行疾病的病理性研究具有重要意义。
In this paper, our aim is to construct FGF1 activated and inhibited up-and down-stream network in chimpanzeeand and human left cerebrum separately. We used microarrays containing 12,558 genes from 15 chimpanzee and 14 human left cerebrum samples in GEO data set. We identified significant expressed genes markers using significant analysis of microarrays. We normalized data by log2 and analysed by cluster analysis method. First, we established total network of 441 significant high and low expression molecules (fold change≥2) from 12,558 genes by GRNInfer. Second, we identified different high-and. low-expression FGF1 network from our total constructed network in chimpanzee and human left cerebrum. Third, we identified FGF1 up- and down-stream network in chimpanzee and human left cerebrum. Fourth, we further identified activated and inhibited molecules from FGF1 up- and down-stream network in chimpanzee and human left cerebrum. Our methods for biological analysis have got a high evaluation by experts in the biomedical field and we have published several papers in international journals indexed by SCI, such as Cell Biochemistry and Biophysics (impact factor 4.311), Journal of Cellular Biochemistry (impact factor 3.121), Cell Proliferation (impact factor 2.742), Cellular and Molecular Neurobiology (impact factor 2.423).
In this paper, we find that FGF1 is related to extracellular region, extracellular matrix (sensu Metazoa), extracellular space, protein binding, growth factor activity, heparin binding; angiogenesis, induction of an organ, signal transduction, development, cell proliferation, fibroblast growth factor receptor signaling pathway, morphogenesis, cell differentiation, lung development, positive regulation of epithelial cell proliferation (GO database). We constructed the low-expression fibroblast growth factor 1 (FGF1) DNA damage-mediated double-strand break combination repair coupling cell division to telomere maintenance for anti-apoptosis network and low-expression fibroblast growth factor 1 (FGF1) inhibited network of innate immunity-driven transcription coupling telomere maintenance via telomere shortening for regulation of apoptosis in chimpanzee left cerebrum compared with high-expression (fold change≥2) human left cerebrum. And we also constructed the high-expression fibroblast growth factor 1 (FGF1) defense response-mediated migration coupling signal with transport to oxidative metabolism for dendrite development network and high-expression fibroblast growth factor 1 (FGF1) inhibited network of migration coupling DNA repair to transcription for positive regulation o axon extension in human left cerebrum compared with low-expression (fold change≥2 chimpanzee left cerebrum. Our result showed that upstream C10ORF10, CDC25B, LOH11CR2A, RAD50, SAPS2, STAMBP activated FGF1; AL049278, AL080232, CFHR1, CTBP1, DDX3Y, RNF2, RPP14, SARM1, TERF1_1 inhibited FGF1 and the downstream FGF1- activated & FGF1-inhibited have no results in chimpanzee lef cerebrum. Our result also showed that upstream CTRL, GPD1, LGALS3BP, MAP1B_3, PCDHGA8, PCSK6, PDIA2 activated FGF1; DTNA, FOXN3_1, MAPT, NAIP, NR1D2_2, SLC25A46, SMG1 inhibited FGF1 and the downstream FGF1 activated MGC15523, NUPR1, UBXD2 and FGF1 inhibited ISCA1, PSMA4, U79289 in human left cerebrum. Our research for fibroblast growth factor-1 has an important role on neurodegenerative disease and clinical treatment, and is helpful for the use of genetic research for diseases of pathological significance.
在本文中,我们通过GO数据库中的基因数据分析发现,分子FGF1的相关模块包括：细胞外区,细胞外基质,细胞外空间,蛋白结合,生长因子活性,肝素结合,血管生成,器官诱导,信号传导,发育,细胞增殖,成细胞生长因子受体信号通路,形态发生,细胞分化,肺发育,上皮细胞增殖的正调控。我们通过将黑猩猩的左脑和人类左脑进行比较,从而在黑猩猩的左脑中分别构建了低表达的成纤维细胞生长因子1 (FGF1)的DNA损伤介导的双链断裂重组修复,耦合了细胞分裂到端粒维持的抗凋亡网络和成纤维细胞生长因子1 (FGF1)的先天免疫驱动的转录耦合端粒维持的缩短导致细胞凋亡的调控网络。而成纤维细胞生长因子1 (FGF1)在人类左脑中,当基因表达改变最小倍数设为2倍时表现为高表达的特性。我们在人类左脑中分别构建了高表达的成纤维细胞生长因子1 (FGF1)的防御响应介导的迁移耦合绑定运输的信号到氧化代谢的诱导树突发育网络和高表达的成纤维细胞生长因子1 (FGF1)的DNA修复的迁移耦合到轴突扩建正调控转录抑制网络。我们的研究结果表明,在黑猩猩左脑中,上游激活网络：分子C10ORF10, CDC25B, LOH11CR2A, RAD50, SAPS2, STAMBP激活FGF1;而在下游的激活网络中,FGF1没有激活任何分子；上游抑制网络：AL049278, AL080232, CFHR1, CTBP1, DDX3Y, RNF2, RPP14, SARM1, TERF1_1抑制FGF1;而下游抑制网络没有相应的结果。在人类的左脑中,上游激活网络：分子CTRL, GPD1, LGALS3BP, MAP1B_3, PCDHGA8, PCSK6, PDIA2激活FGF1;而在下游的激活网络中,FGF1激活分子MGC15523, NUPR1, UBXD2;上游网络：DTNA, FOXN3_1, MAPT, NAIP, NR1D2_2, SLC25A46, SMG1抑制FGF1;而下游网络：FGF1抑制分子ISCA1, PSMA4, U79289。我们对成纤维细胞生长因子1 (FGF1)的研究对于神经退化性疾病的研究以及临床治疗具有重要作用,对于利用基因进行疾病的病理性研究具有重要意义。
In this paper, our aim is to construct FGF1 activated and inhibited up-and down-stream network in chimpanzeeand and human left cerebrum separately. We used microarrays containing 12,558 genes from 15 chimpanzee and 14 human left cerebrum samples in GEO data set. We identified significant expressed genes markers using significant analysis of microarrays. We normalized data by log2 and analysed by cluster analysis method. First, we established total network of 441 significant high and low expression molecules (fold change≥2) from 12,558 genes by GRNInfer. Second, we identified different high-and. low-expression FGF1 network from our total constructed network in chimpanzee and human left cerebrum. Third, we identified FGF1 up- and down-stream network in chimpanzee and human left cerebrum. Fourth, we further identified activated and inhibited molecules from FGF1 up- and down-stream network in chimpanzee and human left cerebrum. Our methods for biological analysis have got a high evaluation by experts in the biomedical field and we have published several papers in international journals indexed by SCI, such as Cell Biochemistry and Biophysics (impact factor 4.311), Journal of Cellular Biochemistry (impact factor 3.121), Cell Proliferation (impact factor 2.742), Cellular and Molecular Neurobiology (impact factor 2.423).
In this paper, we find that FGF1 is related to extracellular region, extracellular matrix (sensu Metazoa), extracellular space, protein binding, growth factor activity, heparin binding; angiogenesis, induction of an organ, signal transduction, development, cell proliferation, fibroblast growth factor receptor signaling pathway, morphogenesis, cell differentiation, lung development, positive regulation of epithelial cell proliferation (GO database). We constructed the low-expression fibroblast growth factor 1 (FGF1) DNA damage-mediated double-strand break combination repair coupling cell division to telomere maintenance for anti-apoptosis network and low-expression fibroblast growth factor 1 (FGF1) inhibited network of innate immunity-driven transcription coupling telomere maintenance via telomere shortening for regulation of apoptosis in chimpanzee left cerebrum compared with high-expression (fold change≥2) human left cerebrum. And we also constructed the high-expression fibroblast growth factor 1 (FGF1) defense response-mediated migration coupling signal with transport to oxidative metabolism for dendrite development network and high-expression fibroblast growth factor 1 (FGF1) inhibited network of migration coupling DNA repair to transcription for positive regulation o axon extension in human left cerebrum compared with low-expression (fold change≥2 chimpanzee left cerebrum. Our result showed that upstream C10ORF10, CDC25B, LOH11CR2A, RAD50, SAPS2, STAMBP activated FGF1; AL049278, AL080232, CFHR1, CTBP1, DDX3Y, RNF2, RPP14, SARM1, TERF1_1 inhibited FGF1 and the downstream FGF1- activated & FGF1-inhibited have no results in chimpanzee lef cerebrum. Our result also showed that upstream CTRL, GPD1, LGALS3BP, MAP1B_3, PCDHGA8, PCSK6, PDIA2 activated FGF1; DTNA, FOXN3_1, MAPT, NAIP, NR1D2_2, SLC25A46, SMG1 inhibited FGF1 and the downstream FGF1 activated MGC15523, NUPR1, UBXD2 and FGF1 inhibited ISCA1, PSMA4, U79289 in human left cerebrum. Our research for fibroblast growth factor-1 has an important role on neurodegenerative disease and clinical treatment, and is helpful for the use of genetic research for diseases of pathological significance.
引文
1. Storey., J.D., A direct approach to false discovery rates. J. Roy. Stat. Soc., Ser. B,2002.64:p. 479-498.
2. Wang, L., et al., Survivin (BIRC5) cell cycle computational network in human no-tumor hepatitis/cirrhosis and hepatocellular carcinoma transformation. J Cell Biochem,2011.
3. Wang, Y., et al., Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics,2006.22(19):p.2413-20.
4. Sun, L., et al., Glycogen Debranching Enzyme 6 (AGL), Enolase 1 (ENOSF1), Ectonucleotide Pyrophosphatase 2 (ENPP2_1), Glutathione S-Transferase 3 (GSTM3_3) and Mannosidase (MAN2B2) Metabolism Computational Network Analysis Between Chimpanzee and Human Left Cerebrum. Cell Biochem Biophys,2011.
5. Amato, S. and H.Y. Man, Bioenergy sensing in the brain:The role of AMP-activated protein kinase in neuronal metabolism, development and neurological diseases. Cell Cycle,2011.10(20): p.3452-60.
6. Bantubungi, K., J. Prawitt, and B. Staels, Control of metabolism by nutrient-regulated nuclear receptors acting in the brain. J Steroid Biochem Mol Biol,2011.
7. Gobel, B. and D. Langemann, Systemic investigation of a brain-centered model of the human energy metabolism. Theory Biosci,2011.130(1):p.5-18.
8. Irwin, R.W., et al., Progesterone and estrogen regulate oxidative metabolism in brain mitochondria. Endocrinology,2008.149(6):p.3167-75.
9. Li, L., et al., The requirement of extracellular signal-related protein kinase pathway in the activation of hypoxia inducible factor 1 alpha in the developing rat brain after hypoxia-ischemia. Acta Neuropathol,2008.115(3):p.297-303.
10. Ueno, A., et al., Brain activity in an awake chimpanzee in response to the sound of her own name. Biol Lett,2011.6(3):p.311-3.
11. Wang, Y.D., et al., Brain derived neurotrophic factor induces endothelial cells angiogenesis through AKT and ERKl/2 signal pathway. Zhongguo Shi Yan Xue Ye Xue Za Zhi,2008.16(1):p. 175-80.
12. Amenta, F. and S.K. Tayebati, Pathways of acetylcholine synthesis, transport and release as targets for treatment of adult-onset cognitive dysfunction. Curr Med Chem,2008.15(5):p. 488-98.
13. Sau, D., et al., Dysregulation of axonal transport and motorneuron diseases. Biol Cell.103(2):p. 87-107.
14. Masliah, E., et al., Deficient glutamate transport is associated with neurodegeneration in Alzheimer's disease. Ann Neurol,1996.40(5):p.759-66.
15. Keller, J.N., et al., 17Beta-estradiol attenuates oxidative impairment of synaptic Na+/K+-ATPase activity, glucose transport, and glutamate transport induced by amyloid beta-peptide and iron. Neurosci Res,1997.50(4):p.522-30.
16. Monfort, P., B. Piedrafita, and V. Felipo, Transport of AMPA receptors during long-terr potentiation is impaired in rats with hepatic encephalopathy. Neurochem Int,2009.55(7): 514-20.
17. Black, M.D., et al., Procognitive and antipsychotic efficacy of glycine transport 1 inhibitor. (GlyTl) in acute and neurodevelopmental models of schizophrenia:latent inhibition studies, the rat. Psychopharmacology (Berl),2009.202(1-3):p.385-96.
18. Huang, J., et al., Interferon a-Inducible Protein 27 Computational Network Construction and Comparison between the Frontal Cortex of HIV Encephalitis (HIVE) and HIVE-Control Patient The Open Genomics Journal 2010.3(1875-693X):p.1-8.
19. Huang, J.X., L. Wang, and M.H. Jiang, TNFRSF11B computational development networ construction and analysis between frontal cortex of HIV encephalitis (HIVE) and HIVE-contro patients. J Inflamm (Lond),2010.7:p.50.
20. Sun, Y., et al., Secreted phosphoprotein 1 upstream invasive network construction and analysis lung adenocarcinoma compared with human normal adjacent tissues by integrativ biocomputation. Cell Biochem Biophys,2010.56(2-3):p.59-71.
21. Sun, Y., L. Wang, and L. Lui, Integrative decomposition procedure and Kappa statistics set up ATF2 ion binding module in Malignant Pleural Mesothelioma (MPM). Frontiers of Electrical and Electronic Engineering in China,2008.3(4):p.381-387.
22. Wang, L., J. Huang, and M. Jiang, RRM2 computational phosphoprotein network constructior and analysis between no-tumor hepatitis/cirrhotic liver tissues and Human Hepatocellulai Carcinoma (HCC). Cell Physiol Biochem,2010.26(3):p.303-10.
23. Wang, L., et al., AFP computational secreted network construction and analysis between humar hepatocellular carcinoma (HCC) and no-tumor hepatitis/cirrhotic liver tissues. Tumour Biol 2010.31(5):p.417-25.
24. Wang, L., et al., FOS proliferating network construction in early colorectal cancer (CRC) basec on integrative significant function cluster and inferring analysis. Cancer Invest,2009.27(8): 816-24.
25. Wang, L., et al., Integrative decomposition procedure and Kappa statistics for the distinguishec single molecular network construction and analysis. J Biomed Biotechnol,2009.2009: 726-728.
26. Sun, T. and C.A. Walsh, Molecular approaches to brain asymmetry and handedness. Nat Rev Neurosci,2006.7(8):p.655-62.
27. Gu, J. and X. Gu, Induced gene expression in human brain after the split from chimpanzee. Trends Genet,2003.19(2):p.63-5.
28. Buxhoeveden, D.P. and M.F. Casanova, The minicolumn and evolution of the brain. Brain Behav Evol,2002.60(3):p.125-51.
29. Preuss, T.M. and G.Q. Coleman, Human-specific organization of primary visual cortex: alternating compartments of dense Cat-301 and calbindin immunoreactivity in layer 4A. Cereb Cortex,2002.12(7):p.671-91.
30. Caceres, M., et al., Elevated gene expression levels distinguish human from non-human primate brains. Proc Natl Acad Sci U S A,2003.100(22):p.13030-5.
31. Ahmed, M., et al., Mismatch brain response to speech sound changes in rats. Front Psychol,2011. 2:p.283.
32. Bantubungi, K., J. Prawitt, and B. Staels, Control of metabolism by nutrient-regulated nuclear receptors acting in the brain. J Steroid Biochem Mol Biol,2011.
33. Irwin, R.W., et al., Progesterone and estrogen regulate oxidative metabolism in brain mitochondria. Endocrinology,2008.149(6):p.3167-75.
34. Yorozu, S., et al., Distinct sensory representations of wind and near-field sound in the Drosophila brain. Nature,2009.458(7235):p.201-5.
35. Monfort, P., B. Piedrafita, and V. Felipo, Transport of AMPA receptors during long-term potentiation is impaired in rats with hepatic encephalopathy. Neurochem Int,2009.55(7):p. 514-20.
36. Toga, A.W. and R.C. Collins, Glucose metabolism increases in visual pathways following habituation. Physiol Behav,1981.27(5):p.825-34.
37. Maya Vetencourt, J.F., et al., Serotonin triggers a transient epigenetic mechanism that reinstates adult visual cortex plasticity in rats. Eur J Neurosci,2011.33(1):p.49-57.
38. Storey., J.D., A direct approach to false discovery rates. J. Roy. Stat. Soc., Ser. B,2002.64:p. 479-498.
39. Wang, L., et al., AFP computational secreted network construction and analysis between human hepatocellular carcinoma (HCC) and no-tumor hepatitis/cirrhotic liver tissues. Tumour Biol, 2010.31(5):p.417-25.
40. Wang, L., et al., FOS proliferating network construction in early colorectal cancer (CRC) based on integrative significant function cluster and inferring analysis. Cancer Invest,2009.27(8):p. 816-24.
41. Gobel, B. and D. Langemann, Systemic investigation of a brain-centered model of the human energy metabolism. Theory Biosci,2011.130(1):p.5-18.
42. Oliveira, C.S., et al., The activation of ERK1/2 and p38 mitogen-activated protein kinases is dynamically regulated in the developing rat visual system. Int J Dev Neurosci,2008.26(3-4):p. 355-62.
43. Prestwich, K.N. and K. O'Sullivan, Simultaneous measurement of metabolic and acoustic power and the efficiency of sound production in two mole cricket species (Orthoptera:Gryllotalpidae). J Exp Biol,2005.208(Pt 8):p.1495-512.
44. Black, M.D., et al., Procognitive and antipsychotic efficacy of glycine transport 1 inhibitors (GlyT1) in acute and neurodevelopmental models of schizophrenia:latent inhibition studies in the rat. Psychopharmacology (Berl),2009.202(1-3):p.385-96.
45. Hessel, E., et al., Signal transduction in the visual cascade involves specific lipid-protein interactions. J Biol Chem,2003.278(25):p.22853-60.
46. Owe-Young, R., et al., Kynurenine pathway metabolism in human blood-brain-barrier cells: implications for immune tolerance and neurotoxicity. J Neurochem,2008.105(4):p.1346-57.
47. Caceres, M., et al., Elevated gene expression levels distinguish human from non-human primate brains. Proc Natl Acad Sci U S A,2003.100(22):p.13030-5.
48. Niehusmann, P., et al., Mitochondrial dysfunction due to Leber's hereditary optic neuropathy as a cause of visual loss during assessment for epilepsy surgery. Epilepsy Behav,2011.20(1):p 38-43.
49. Battelle, B.A. and M.K. Hart, Histamine metabolism in the visual system of the horseshoe crat Limulus polyphemus. Comp Biochem Physiol A Mol Integr Physiol,2002.133(1):p.135-42.
50. Sau, D., et al., Dysregulation of axonal transport and motorneuron diseases. Biol Cell.103(2): 87-107.
51. Amato, S. and H.Y. Man, Bioenergy sensing in the brain:The role of AMP-activated proteir kinase in neuronal metabolism, development and neurological diseases. Cell Cycle,2011.10(20) p.3452-60.
52. Li, L., et al., The requirement of extracellular signal-related protein kinase pathway in the activation of hypoxia inducible factor 1 alpha in the developing rat brain after hypoxia-ischemia Acta Neuropathol,2008.115(3):p.297-303.
53. Wang, Y.D., et al., Brain derived neurotrophic factor induces endothelial cells angiogenesis through AKT and ERK1/2 signal pathway. Zhongguo Shi Yan Xue Ye Xue Za Zhi,2008.16(1): 175-80.
54. Hessel, E., et al., Signal transduction in the visual cascade involves specific lipid-protein interactions. J Biol Chem,2003.278(25):p.22853-60.
55. Alberghina, M. and M. Viola, Region-selective decline of in vivo lipid synthesis in the aged rat visual system. Mol Chem Neuropathol,1989.11(2):p.109-22.
56. Wang, L., et al., Integrative decomposition procedure and Kappa statistics for the distinguished single molecular network construction and analysis. J Biomed Biotechnol,2009.2009:p 726-728.
57. Dahlhaus, M., et al., The synaptic proteome during development and plasticity of the mouse visual cortex. Mol Cell Proteomics,2011.10(5):p. M110 005413.
58. Wang, Y, et al., Inferring gene regulatory networks from multiple microarray datasets, Bioinformatics,2006.22(19):p.2413-20.
2. Wang, L., et al., Survivin (BIRC5) cell cycle computational network in human no-tumor hepatitis/cirrhosis and hepatocellular carcinoma transformation. J Cell Biochem,2011.
3. Wang, Y., et al., Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics,2006.22(19):p.2413-20.
4. Sun, L., et al., Glycogen Debranching Enzyme 6 (AGL), Enolase 1 (ENOSF1), Ectonucleotide Pyrophosphatase 2 (ENPP2_1), Glutathione S-Transferase 3 (GSTM3_3) and Mannosidase (MAN2B2) Metabolism Computational Network Analysis Between Chimpanzee and Human Left Cerebrum. Cell Biochem Biophys,2011.
5. Amato, S. and H.Y. Man, Bioenergy sensing in the brain:The role of AMP-activated protein kinase in neuronal metabolism, development and neurological diseases. Cell Cycle,2011.10(20): p.3452-60.
6. Bantubungi, K., J. Prawitt, and B. Staels, Control of metabolism by nutrient-regulated nuclear receptors acting in the brain. J Steroid Biochem Mol Biol,2011.
7. Gobel, B. and D. Langemann, Systemic investigation of a brain-centered model of the human energy metabolism. Theory Biosci,2011.130(1):p.5-18.
8. Irwin, R.W., et al., Progesterone and estrogen regulate oxidative metabolism in brain mitochondria. Endocrinology,2008.149(6):p.3167-75.
9. Li, L., et al., The requirement of extracellular signal-related protein kinase pathway in the activation of hypoxia inducible factor 1 alpha in the developing rat brain after hypoxia-ischemia. Acta Neuropathol,2008.115(3):p.297-303.
10. Ueno, A., et al., Brain activity in an awake chimpanzee in response to the sound of her own name. Biol Lett,2011.6(3):p.311-3.
11. Wang, Y.D., et al., Brain derived neurotrophic factor induces endothelial cells angiogenesis through AKT and ERKl/2 signal pathway. Zhongguo Shi Yan Xue Ye Xue Za Zhi,2008.16(1):p. 175-80.
12. Amenta, F. and S.K. Tayebati, Pathways of acetylcholine synthesis, transport and release as targets for treatment of adult-onset cognitive dysfunction. Curr Med Chem,2008.15(5):p. 488-98.
13. Sau, D., et al., Dysregulation of axonal transport and motorneuron diseases. Biol Cell.103(2):p. 87-107.
14. Masliah, E., et al., Deficient glutamate transport is associated with neurodegeneration in Alzheimer's disease. Ann Neurol,1996.40(5):p.759-66.
15. Keller, J.N., et al., 17Beta-estradiol attenuates oxidative impairment of synaptic Na+/K+-ATPase activity, glucose transport, and glutamate transport induced by amyloid beta-peptide and iron. Neurosci Res,1997.50(4):p.522-30.
16. Monfort, P., B. Piedrafita, and V. Felipo, Transport of AMPA receptors during long-terr potentiation is impaired in rats with hepatic encephalopathy. Neurochem Int,2009.55(7): 514-20.
17. Black, M.D., et al., Procognitive and antipsychotic efficacy of glycine transport 1 inhibitor. (GlyTl) in acute and neurodevelopmental models of schizophrenia:latent inhibition studies, the rat. Psychopharmacology (Berl),2009.202(1-3):p.385-96.
18. Huang, J., et al., Interferon a-Inducible Protein 27 Computational Network Construction and Comparison between the Frontal Cortex of HIV Encephalitis (HIVE) and HIVE-Control Patient The Open Genomics Journal 2010.3(1875-693X):p.1-8.
19. Huang, J.X., L. Wang, and M.H. Jiang, TNFRSF11B computational development networ construction and analysis between frontal cortex of HIV encephalitis (HIVE) and HIVE-contro patients. J Inflamm (Lond),2010.7:p.50.
20. Sun, Y., et al., Secreted phosphoprotein 1 upstream invasive network construction and analysis lung adenocarcinoma compared with human normal adjacent tissues by integrativ biocomputation. Cell Biochem Biophys,2010.56(2-3):p.59-71.
21. Sun, Y., L. Wang, and L. Lui, Integrative decomposition procedure and Kappa statistics set up ATF2 ion binding module in Malignant Pleural Mesothelioma (MPM). Frontiers of Electrical and Electronic Engineering in China,2008.3(4):p.381-387.
22. Wang, L., J. Huang, and M. Jiang, RRM2 computational phosphoprotein network constructior and analysis between no-tumor hepatitis/cirrhotic liver tissues and Human Hepatocellulai Carcinoma (HCC). Cell Physiol Biochem,2010.26(3):p.303-10.
23. Wang, L., et al., AFP computational secreted network construction and analysis between humar hepatocellular carcinoma (HCC) and no-tumor hepatitis/cirrhotic liver tissues. Tumour Biol 2010.31(5):p.417-25.
24. Wang, L., et al., FOS proliferating network construction in early colorectal cancer (CRC) basec on integrative significant function cluster and inferring analysis. Cancer Invest,2009.27(8): 816-24.
25. Wang, L., et al., Integrative decomposition procedure and Kappa statistics for the distinguishec single molecular network construction and analysis. J Biomed Biotechnol,2009.2009: 726-728.
26. Sun, T. and C.A. Walsh, Molecular approaches to brain asymmetry and handedness. Nat Rev Neurosci,2006.7(8):p.655-62.
27. Gu, J. and X. Gu, Induced gene expression in human brain after the split from chimpanzee. Trends Genet,2003.19(2):p.63-5.
28. Buxhoeveden, D.P. and M.F. Casanova, The minicolumn and evolution of the brain. Brain Behav Evol,2002.60(3):p.125-51.
29. Preuss, T.M. and G.Q. Coleman, Human-specific organization of primary visual cortex: alternating compartments of dense Cat-301 and calbindin immunoreactivity in layer 4A. Cereb Cortex,2002.12(7):p.671-91.
30. Caceres, M., et al., Elevated gene expression levels distinguish human from non-human primate brains. Proc Natl Acad Sci U S A,2003.100(22):p.13030-5.
31. Ahmed, M., et al., Mismatch brain response to speech sound changes in rats. Front Psychol,2011. 2:p.283.
32. Bantubungi, K., J. Prawitt, and B. Staels, Control of metabolism by nutrient-regulated nuclear receptors acting in the brain. J Steroid Biochem Mol Biol,2011.
33. Irwin, R.W., et al., Progesterone and estrogen regulate oxidative metabolism in brain mitochondria. Endocrinology,2008.149(6):p.3167-75.
34. Yorozu, S., et al., Distinct sensory representations of wind and near-field sound in the Drosophila brain. Nature,2009.458(7235):p.201-5.
35. Monfort, P., B. Piedrafita, and V. Felipo, Transport of AMPA receptors during long-term potentiation is impaired in rats with hepatic encephalopathy. Neurochem Int,2009.55(7):p. 514-20.
36. Toga, A.W. and R.C. Collins, Glucose metabolism increases in visual pathways following habituation. Physiol Behav,1981.27(5):p.825-34.
37. Maya Vetencourt, J.F., et al., Serotonin triggers a transient epigenetic mechanism that reinstates adult visual cortex plasticity in rats. Eur J Neurosci,2011.33(1):p.49-57.
38. Storey., J.D., A direct approach to false discovery rates. J. Roy. Stat. Soc., Ser. B,2002.64:p. 479-498.
39. Wang, L., et al., AFP computational secreted network construction and analysis between human hepatocellular carcinoma (HCC) and no-tumor hepatitis/cirrhotic liver tissues. Tumour Biol, 2010.31(5):p.417-25.
40. Wang, L., et al., FOS proliferating network construction in early colorectal cancer (CRC) based on integrative significant function cluster and inferring analysis. Cancer Invest,2009.27(8):p. 816-24.
41. Gobel, B. and D. Langemann, Systemic investigation of a brain-centered model of the human energy metabolism. Theory Biosci,2011.130(1):p.5-18.
42. Oliveira, C.S., et al., The activation of ERK1/2 and p38 mitogen-activated protein kinases is dynamically regulated in the developing rat visual system. Int J Dev Neurosci,2008.26(3-4):p. 355-62.
43. Prestwich, K.N. and K. O'Sullivan, Simultaneous measurement of metabolic and acoustic power and the efficiency of sound production in two mole cricket species (Orthoptera:Gryllotalpidae). J Exp Biol,2005.208(Pt 8):p.1495-512.
44. Black, M.D., et al., Procognitive and antipsychotic efficacy of glycine transport 1 inhibitors (GlyT1) in acute and neurodevelopmental models of schizophrenia:latent inhibition studies in the rat. Psychopharmacology (Berl),2009.202(1-3):p.385-96.
45. Hessel, E., et al., Signal transduction in the visual cascade involves specific lipid-protein interactions. J Biol Chem,2003.278(25):p.22853-60.
46. Owe-Young, R., et al., Kynurenine pathway metabolism in human blood-brain-barrier cells: implications for immune tolerance and neurotoxicity. J Neurochem,2008.105(4):p.1346-57.
47. Caceres, M., et al., Elevated gene expression levels distinguish human from non-human primate brains. Proc Natl Acad Sci U S A,2003.100(22):p.13030-5.
48. Niehusmann, P., et al., Mitochondrial dysfunction due to Leber's hereditary optic neuropathy as a cause of visual loss during assessment for epilepsy surgery. Epilepsy Behav,2011.20(1):p 38-43.
49. Battelle, B.A. and M.K. Hart, Histamine metabolism in the visual system of the horseshoe crat Limulus polyphemus. Comp Biochem Physiol A Mol Integr Physiol,2002.133(1):p.135-42.
50. Sau, D., et al., Dysregulation of axonal transport and motorneuron diseases. Biol Cell.103(2): 87-107.
51. Amato, S. and H.Y. Man, Bioenergy sensing in the brain:The role of AMP-activated proteir kinase in neuronal metabolism, development and neurological diseases. Cell Cycle,2011.10(20) p.3452-60.
52. Li, L., et al., The requirement of extracellular signal-related protein kinase pathway in the activation of hypoxia inducible factor 1 alpha in the developing rat brain after hypoxia-ischemia Acta Neuropathol,2008.115(3):p.297-303.
53. Wang, Y.D., et al., Brain derived neurotrophic factor induces endothelial cells angiogenesis through AKT and ERK1/2 signal pathway. Zhongguo Shi Yan Xue Ye Xue Za Zhi,2008.16(1): 175-80.
54. Hessel, E., et al., Signal transduction in the visual cascade involves specific lipid-protein interactions. J Biol Chem,2003.278(25):p.22853-60.
55. Alberghina, M. and M. Viola, Region-selective decline of in vivo lipid synthesis in the aged rat visual system. Mol Chem Neuropathol,1989.11(2):p.109-22.
56. Wang, L., et al., Integrative decomposition procedure and Kappa statistics for the distinguished single molecular network construction and analysis. J Biomed Biotechnol,2009.2009:p 726-728.
57. Dahlhaus, M., et al., The synaptic proteome during development and plasticity of the mouse visual cortex. Mol Cell Proteomics,2011.10(5):p. M110 005413.
58. Wang, Y, et al., Inferring gene regulatory networks from multiple microarray datasets, Bioinformatics,2006.22(19):p.2413-20.