Temporal and spatial patterns of gene profiles during chondrogenic differentiation

IEEE Journal of Biomedical and Health Informatics

Volumn 18, Issue 3, 2014, Pages 799-809

  Skreti, G ^a   Bei, E S ^a   Kalantzaki, K ^a   Zervakis, M ^a  

^a TECHNICAL UNIVERSITY OF CRETE   (Greece)

Author keywords

Chondrogenic differentiation; gene networks; mixed clustering; spatial profile; Temporal profile

Indexed keywords

BONE; GENE EXPRESSION; STEM CELLS;

CHONDROGENIC DIFFERENTIATION; GENE NETWORKS; MIXED CLUSTERING; SPATIAL PROFILES; TEMPORAL PROFILE;

CELL CULTURE;

TRANSCRIPTOME;

BIOLOGY; BONE MARROW CELL; CARTILAGE CELL; CELL CULTURE; CELL DIFFERENTIATION; CLUSTER ANALYSIS; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETICS; HUMAN; MESENCHYMAL STROMA CELL; PHYSIOLOGY; PROCEDURES;

BONE MARROW CELLS; CELL DIFFERENTIATION; CELLS, CULTURED; CHONDROCYTES; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE REGULATORY NETWORKS; HUMANS; MESENCHYMAL STROMAL CELLS; TRANSCRIPTOME;

EID: 84900557470     PISSN: 21682194     EISSN: None     Source Type: Journal    
DOI: 10.1109/JBHI.2014.2305770     Document Type: Article

References (34)

1. S. Imoto and S. Miyano, "Statistical analysis o small set of time-ordered gene expression data using linear splines," Bioinformatics, vol. 18, no. 11, pp. 1477-1485, Apr. 2002. (Pubitemid 35414539)
2. H. Liu, S. Tarima, A. S. Borders, T. V Getchell, M. L. Getchell, and A. J. Stromberg, "Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments," BMC Bioinform. , vol. 6, no. 106, pp. 1-69, Apr. 2005.
3. S. D. Peddada, E. K. Lobenhofer, L. Li, C. A. Afshari, C. R. Weinberg, and D. M. Umbach, "Gene selection and clustering for time-course and dose-response microarray experiments using order-restricted inference," Bioinformatics, vol. 19, no. 7, pp. 834-841, Nov. 2003. (Pubitemid 36582399)
4. S. G. Yi, Y. J. Joo, and T. Park, "Rank-based analysis for the time-course microarray data," J. Bioinform. Comput. Biol. , vol. 7, no. 1, pp. 75-91, Sep. 2009.
5. S. G. Yi, Y. J. Joo, and T. Park, "Rank-based clustering analysis for the time-course microarray data," J. Bioinform. Comput. Biol. , vol. 7, no. 1, pp. 75-91, Aug. 2009.
6. S. C. Madeira, M. C. Teixeira, I. Śa-Correia, and A. L. Oliveira, "Identification of regulatory modules in time series gene expression data using a linear time biclustering algorithm," IEEE /ACM Trans. Comput. Biol. Bioinform. , vol. 7, no. 1, pp. 153-165, Oct. 2007.
7. A. V. Carreiro, O. Anunciaçao, J. A. Carriço, and S. C. Madeira, "Prognostic prediction through biclustering-based classification of clinical gene expression time series," J. Integr. Bioinform. , vol. 8, no. 3, no. 175, pp. 1-17, Jan. 2011.
8. G. Skreti, E. S. Bei, and M. Zervakis, "Shape-influenced clustering of dynamic patterns of gene profiles," in Proc. IEEE Eng. Med. Biol. Soc Conf. , Jan. 2012, vol. 2012, pp. 1238-1241.
9. L. Ji and K. L. Tan, "Mining gene expression data for positive and negative co-regulated gene clusters," Bioinformatics, vol. 20, no. 16, pp. 2711-2718, Apr. 2004. (Pubitemid 39530158)
10. L. Ji and K. L. Tan, "Identifying time-lagged gene clusters using gene expression data," Bioinformatics, vol. 21, no. 4, pp. 509-516, Sep. 2005. (Pubitemid 40310238)
11. K. D. Kalantzaki, E. S. Bei, M. Garofalakis, and M. Zervakis, "Biological interaction networks based on sparse temporal expansion of graphical models," in Proc. 12th IEEE Int. Conf. BioInform. BioEngineering, 2012, pp. 460-465.
12. W. Jiang, X. Li, S. Rao, L. Wang, L. Du, C. Li, C. Wu, H. Wang, Y. Wang, and B. Yang, "Constructing disease-specific gene networks using pairwise relevance metric: Application to colon cancer identifies interleukin 8, desmin, and enolase 1 as the central elements," BMC Syst. Biol. , vol. 2, no. 72, pp. 1-15, Aug. 2008.
13. N. Friedman, M. Linial, I. Nachman, and D. Pe'er, "Using Bayesian networks to analyze expression data," J. Comput. Biol. , vol. 7, no. 3-4, pp. 601-620, Jan. 2000.
14. J. Hu, J. Wan, L. Hackler,D. J. Zack, and J. Qian, "Computational analysis of tissue-specific gene networks: Application to murine retinal functional studies," Bioinformatics, vol. 26, no. 18, pp. 2289-2297, Jul. 2010.
15. F. Browne, H. Wang, H. Zheng, and F. Azuaje, "A knowledge-driven probabilistic framework for the prediction of protein-protein interaction networks," Comput. Biol. Med. , vol. 40, no. 3, pp. 306-317, Jan. 2010.
16. S. Bulashevska, A. Bulashevska, and R. Eils, "Bayesian statistical modelling of human protein interaction network incorporating protein disorder information," BMC Bioinform. , vol. 11, no. 46, pp. 1-15, Jan. 2010.
17. C. C. Wu, S. Asgharzadeh, T. J. Triche, and D. Z. D'Argenio, "Prediction of human functional genetic networks from heterogeneous data using RVM-based ensemble learning," Bioinformatics, vol. 26, no. 6, pp. 807-813, Feb. 2010.
18. Y.-Q. Qiu, S. Zhang, X.-S. Zhang, and L. Chen, "Detecting disease associated modules and prioritizing active genes based on high throughput data," BMC Bioinform. , vol. 11, no. 26, pp. 1-12, Jan. 2010.
19. H. Wang, D. Mirota, and G. D. Hager, "A generalized Kernel Consensusbased robust estimator," IEEE Trans. Pattern Anal. Mach. Intell. , vol. 32, no. 1, pp. 178-184, Jan. 2010.
20. R. Boscolo, H. Pan, and V. P. Roychowdhury, "Independent component analysis based on nonparametric density estimation," IEEE Trans. Neural Netw. /a Publ. IEEE Neural Netw. Counc. , vol. 15, no. 1, pp. 55-65, Jan. 2004.
21. E. C. Neto, C. T. Ferrara, A. D. Attie, and B. S. Yandell, "Inferring causal phenotype networks from segregating populations," Genetics, vol. 179, no. 2, pp. 1089-1100, Apr. 2008.
22. X. W. Chen, G. Anantha, and X. Wang, "An effective structure learning method for constructing gene networks," Bioinformatics, vol. 22, no. 11, pp. 1367-1374, Mar. 2006. (Pubitemid 43985273)
23. P. Bernstein, C. Sticht, A. Jacobi, C. Liebers, S. Manthey, andM. Stiehler, "Expression pattern differences between osteoarthritic chondrocytes and mesenchymal stem cells during chondrogenic differentiation, " Osteoarthritis Cartilage, vol. 18, no. 12, pp. 1596-1607, Sep. 2010.
24. B. Zhang, S. Kirov, and J. Snoddy, "WebGestalt: an integrated system for exploring gene sets in various biological contexts," Nucleic Acids Res. , vol. 33, pp. W741-W748, Apr. 2005. (Pubitemid 44530021)
25. A. Woods, G. Wang, and F. Beier, "Regulation of chondrocyte differentiation by the actin cytoskeleton and adhesive interactions," J. Cell. Physiol. , vol. 213, no. 1, pp. 1-8, Oct. 2007. (Pubitemid 47378786)
26. B. Rocha, V. Calamia, J. Mateos, P. Ferńandez-Puente, F. J. Blanco, and C. Ruiz-Romero, "Metabolic labeling of human bone marrow mesenchymal stem cells for the quantitative analysis of their chondrogenic differentiation," J. Proteome Res. , vol. 11, no. 11, pp. 5350-5361, Sep. 2012.
27. H. J. Yoo, S. S. Yoon, S. Y. Park, E. Y. Lee, E. B. Lee, J. H. Kim, and Y. W. Song, "Gene expression profile during chondrogenesis in human bone marrow derived mesenchymal stem cells using a cDNA microarray," J. Korean Med. Sci. , vol. 26, no. 7, pp. 851-858, Jul. 2011.
28. M. M. J. Caron, P. J. Emans, M. M. E. Coolsen, L. Voss, D. A. M. Surtel, A. Cremers, L. W. Van Rhijn, and T. J. M. Welting, "Redifferentiation of dedifferentiated human articular chondrocytes: comparison of 2D and 3D cultures," Osteoarthritis Cartilage, vol. 20, no. 10, pp. 1170-1178, Oct. 2012.
29. A. M. Newman, N. B. Gallo, L. S. Hancox, N. J. Miller, C. M. Radeke, M. A. Maloney, J. B. Cooper, G. S. Hageman, D. H. Anderson, L. V Johnson, and M. J. Radeke, "Systems-level analysis of age-related macular degeneration reveals global biomarkers and phenotype-specific functional networks," Genome Med. , vol. 4, no. 2, p. 16, Feb. 2012.
30. J. J. Linderman, "Modeling of G-protein-coupled receptor signaling pathways," J. Biol. Chem. , vol. 284, no. 9, pp. 5427-5431, Feb. 2009.
31. P. S. Mathieu and E. G. Loboa, "Cytoskeletal and focal adhesion influences on mesenchymal stem cell shape, mechanical properties, and differentiation down osteogenic, adipogenic, and chondrogenic pathways," Tissue Eng. Part B Rev. , vol. 18, no. 6, pp. 436-444, Nov. 2012.
32. J. W. Yang, N. De Isla, C. Huselstein, M. N. Sarda-Kolopp, Y. P. L. N. Li, O. Y. Jing-Ping, J. F. Stoltz, and A. Eljaafari, "Evaluation of human MSCs cell cycle, viability and differentiation in micromass culture," Biorheology, vol. 43, no. 3-4, pp. 489-496, 2006. (Pubitemid 44221928)
33. J. J. Cai, E. Borenstein, and D. A. Petrov, "Broker genes in human disease," Genome Biol. Evol. , vol. 2, pp. 815-825, Oct. 2010.
34. A. Goldar, M. C. Marsolier-Kergoat, and O. Hyrien, "Universal temporal profile of replication origin activation in eukaryotes," PLoS One, vol. 4, no. 6, p. e5899, Jan. 2009.