ARN: Recombination and Visualization of Adipogenesis Regulation Network Information

作者: 黄 艳 , 王 力 , 昝林森 :西北农林科技大学动物科技学院,国家肉牛改良中心,陕西 杨凌;

关键词: 脂肪生成数据库重组可视化文本挖掘Adipogenesis Database Recombination Visualization Text Mining


Abstract: 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.

文章引用: 黄 艳 , 王 力 , 昝林森 (2016) ARN数据库:重组和可视化成脂调控网络信息。 计算生物学, 6, 8-17. doi: 10.12677/HJCB.2016.61002


[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.

[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.

[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.

[4] Sarjeant, K. and Stephens, J.M. (2012) Adipogenesis. Cold Spring Harbor Perspectives in Biology, 4, a00841.

[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.

[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.

[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.

[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.

[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.

[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.

[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.

[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.

[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.

[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.

[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 Drabløs 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.

[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.

[20] Cohen, K.B. and Hunter, L. (2008) Getting Started in Text Mining. PLOS Computational Biology, 4, 1-3.

[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.

[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.

[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.

[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.

[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.