ARN数据库：重组和可视化成脂调控网络信息
ARN: Recombination and Visualization of Adipogenesis Regulation Network Information

DOI: 10.12677/HJCB.2016.61002, PP. 8-17

Keywords: 脂肪生成，数据库，重组，可视化，文本挖掘
Adipogenesis, Database, Recombination, Visualization, Text Mining

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Abstract:

肥胖是工业化国家面临的巨大挑战。同时，许多代谢相关的疾病如糖尿病、动脉粥样硬化等也和脂肪的累积息息相关。因此，我们有必要深入理解成脂(脂肪组织形成的过程)的分子机制。然而，信息的碎片化严重阻碍着新的关键基因及通路的识别，于是我们想到要为专业的研究人员提供一个方便易用的成脂调控信息中心。在本研究中，我们通过文本挖掘技术辅以专业人员的人工检查和注释，整理收集来自PubMed数据库的1457篇与成脂分化相关的文章，搭建了一个公开的数据库平台——ARN数据库，截止到2016年2月25日，共收集到与成脂相关的3054个节点，1807条互作关系，10,675条表达记录，并通过miRGate、PAZAR和TRRUST等数据库确定了12,696条可能存在的靶向调控关系，为成脂研究领域的研究者提供了一个快速便捷的可视化信息中心。因此，这个平台将有助于研究者发现成脂调控中的重要基因和通路。
Excessive weight gain and obesity pose significant health challenges to many industrialized na-tions. Many metabolic disorders associated with cardiovascular diseases such as diabetes and atherosclerosis are directly linked to the increased production and size of adipose cells. Under-standing the molecular mechanism that underlies adipogenesis, the process by which adipose or fat tissue is formed, is thus of critical importance. However, the information fragmentation ham-pers the identification of key regulatory genes and pathways. Thus, it is necessary to provide an information center that is quickly and easily accessible to researchers in this field. In this study, we developed a publicly available database and web interface that serves as a resource for adi-pogenesis research. In ARN, nodes (genes and microRNAs) were collected using a text mining procedure followed by manual review and annotation by experts of this field. In total, 3054 nodes, 1807 relations, and 10,675 expression records associated with adipogenesis according to 1457 articles were collected (last update: 29 January 2016). Additionally, we further determined 12,696 possible relations of these nodes due to miRGate, PAZAR and TRRUST. Hence, this plat-form can support the ongoing adipogenesis research and contribute to discovery of key regula-tory genes and pathways.

References

[1]	Hausman, D.B., DiGirolamo, M., Bartness, T.J., Hausman, G.J. and Martin, R.J. (2001) The Biology of White Adipocyte Proliferation. Obesity Research, 2, 239-254. http://dx.doi.org/10.1046/j.1467-789X.2001.00042.x
[2]	Tontonoz. P., Hu, E. and Spiegelman, B.M. (1994) Stimulation of Adipogenesis in Fibroblasts by PPAR Gamma 2, a Lipid-Activated Transcription Factor. Cell, 79, 1147-1156. http://dx.doi.org/10.1016/0092-8674(94)90006-X
[3]	Hu, E., Tontonoz, P. and Spiegelman, B.M. (1995) Transdifferentiation of Myoblasts by the Adipogenic Transcription Factors PPAR Gamma and C/EBP Alpha. Proceedings of the National Academy of Sciences USA, 92, 9856-9860. http://dx.doi.org/10.1073/pnas.92.21.9856
[4]	Sarjeant, K. and Stephens, J.M. (2012) Adipogenesis. Cold Spring Harbor Perspectives in Biology, 4, a00841. http://dx.doi.org/10.1101/cshperspect.a008417
[5]	Rosen, E.D. (2002) The Molecular Control of Adipogenesis, with Special Reference to Lymphatic Pathology. Annals of the New York Academy of Sciences, 979, 143-158, Discussion 188-196. http://dx.doi.org/10.1111/j.1749-6632.2002.tb04875.x
[6]	Wu, Z., Rosen, E.D., Brun, R., Hauser, S., Adelmant, G., Troy, A.E., McKeon, C., Darlington, G.J. and Spiegelman, B.M. (1999) Cross-Regulation of C/EBP Alpha and PPAR Gamma Controls the Transcriptional Pathway of Adipogenesis and Insulin Sensitivity. Molecular Cell, 3, 151-158. http://dx.doi.org/10.1016/S1097-2765(00)80306-8
[7]	Mei, Y., Bian, C., Li, J., Du, Z., Zhou, H., Yang, Z. and Zhao, R.C. (2013) miR-21 Modulates the ERK-MAPK Signaling Pathway by Regulating SPRY2 Expression during Human Me-senchymal Stem Cell Differentiation. Journal of Cellular Biochemistry, 114, 1374-1384. http://dx.doi.org/10.1002/jcb.24479
[8]	Kim, S.Y., Kim, A.Y., Lee, H.W., Son, Y.H., Lee, G.Y., Lee, J.W., Lee, Y.S. and Kim, J.B. (2010) miR-27a Is a Negative Regulator of Adipocyte Differentiation via Suppressing PPARgamma Expression. Biochemical and Biophysical Research Communications, 392, 323-328. http://dx.doi.org/10.1016/j.bbrc.2010.01.012
[9]	Kim, Y.J., Min, T.S., Seo, K.S. and Kim, S.H. (2015) Expression of pref-1/dlk-1 Is Regulated by microRNA-143 in 3T3-L1 Cells. Molecular Biology Reports, 42, 617-624. http://dx.doi.org/10.1007/s11033-014-3807-0
[10]	Esau, C., Kang, X., Peralta, E., Hanson, E., Marcusson, E.G., Ravichandran, L.V., Sun, Y., Koo, S., Perera, R.J., Jain, R., Dean, N.M., Freier, S.M., Bennett, C.F., Lollo, B. and Griffey, R. (2004) MicroRNA-143 Regulates Adipocyte Differentiation. Journal of Biological Chemistry, 279, 52361-52365. http://dx.doi.org/10.1074/jbc.C400438200
[11]	Huang, J., Zhao, L., Xing, L. and Chen, D. (2010) MicroRNA-204 Regulates Runx2 Protein Expression and Mesenchymal Progenitor Cell Differentiation. Stem Cells, 28, 357-364.
[12]	Vailaya, A., Bluvas, P., Kincaid, R., Kuchinsky, A., Creech, M. and Adler, A. (2005) An Architecture for Biological Information Extraction and Representation. Bioinformatics, 21, 430-438. http://dx.doi.org/10.1093/bioinformatics/bti187
[13]	Han, H., Shim, H., Shin, D., Shim, J.E., Ko, Y., Shin, J., Kim, H., Cho, A., Kim, E., Lee, T., Kim, H., Kim, K., Yang, S., Bae, D., Yun, A., Kim, S., Kim, C.Y., Cho, H.J., Kang, B., Shin, S. and Lee, I. (2015) TRRUST: A Reference Database of Human Transcriptional Regulatory Interactions. Scientific Reports, 5, 11432. http://dx.doi.org/10.1038/srep11432
[14]	Portales-Casamar, E., Arenillas, D., Lim, J., Swanson, M.I., Jiang, S., McCallum, A., Kirov, S. and Wasserman, W.W. (2009) PAZAR: A Framework for Collection and Dissemination of Cis-Regulatory Sequence Annotation. Nucleic Acids Research, 37, R207, 1-12.
[15]	Kozomara, A. and Griffiths-Jones, S. (2014) miRBase: Annotating High Confidence microRNAs Using Deep Sequencing Data. Nucleic Acids Research, 42, D68-D73. http://dx.doi.org/10.1093/nar/gkt1181
[16]	McDowall, M.D., Scott, M.S. and Barton, G.J. (2009) PIPs: Human Protein-Protein Interaction Prediction Database. Nucleic Acids Research, 37, D651-D656. http://dx.doi.org/10.1093/nar/gkn870
[17]	Medvedeva, Y.A., Lennartsson, A., Ehsani, R., Kulakovskiy, I.V., Vorontsov, I.E., Panahandeh, P., Khimulya, G. and Kasukawa, T. (2015) FANTOM Consortium, and Drabl？s F. EpiFactors: A Comprehensive Database of Human Epigenetic Factors and Complexes. Database (Oxford), bav067, 1-10.
[18]	Cline, M.S., Smoot, M., Cerami, E., Kuchinsky, A., Landys, N., Workman, C., Christmas, R., Avila-Campilo, I., Creech, M., Gross, B., et al. (2007) Integration of Biological Networks and Gene Expression Data Using Cytoscape. Nature Protocols, 2, 2366-2382. http://dx.doi.org/10.1038/nprot.2007.324
[19]	Cristancho, A.G. and Lazar, M.A. (2011) Forming Functional Fat: A Growing Understanding of Adipocyte Differentiation. Nature Reviews Molecular Cell Biology, 12, 722-734. http://dx.doi.org/10.1038/nrm3198
[20]	Cohen, K.B. and Hunter, L. (2008) Getting Started in Text Mining. PLOS Computational Biology, 4, 1-3. http://dx.doi.org/10.1371/journal.pcbi.0040020
[21]	González-Pérez, A. and López-Bigas, N. (2011) Improving the Assessment of the Outcome of Nonsynonymous SNVs with a Consensus Deleteriousness Score. Condel. The American Journal of Human Genetics, 88, 440-449. http://dx.doi.org/10.1016/j.ajhg.2011.03.004
[22]	Pan, Y. C., Li, C.F., Ko, C.Y., Pan, M.H. and Wang, J.M. (2010) CEBPD Reverses RB/E2F1-Mediated Gene Repression and Participates in HMDB-Induced Apoptosis of Cancer Cells. Clinical Cancer Research, 16, 5770-5780. http://dx.doi.org/10.1158/1078-0432.CCR-10-1025
[23]	Fakhry, M., Hamade, E., Badran, B., Buchet, R. and Magne, D. (2013) Molecular Mechanisms of Mesenchymal Stem Cell Differentiation towards Osteoblasts. World Journal of Stem Cells, 5, 136-148. http://dx.doi.org/10.4252/wjsc.v5.i4.136
[24]	Sun, L., Goff, L.A., Trapnell, C., Alexander, R., Lo, K.A., Hacisuleyman, E., Sauvageau, M., Tazon-Vega, B., Kelley, D.R., Hendrickson, D.G., Yuan, B., Kellis, M., Lodish, H.F. and Rinn, J.L. (2013) Long Noncoding RNAs Regulate Adipogenesis. Proceedings of the National Academy of Sciences USA, 110, 3387-3392. http://dx.doi.org/10.1073/pnas.1222643110
[25]	Chen, J., Cui, X., Shi, C., Chen, L., Yang, L., Pang, L., Zhang, J., Guo, X., Wang, J. and Ji, C. (2015) Differential lncRNA Expression Profiles in Brown and White Adipose Tissues. Molecular Genetics and Genomics, 290, 699-707. http://dx.doi.org/10.1007/s00438-014-0954-x

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