Genome-wide scale-free network inference for Candida albicans

Frontiers in Microbiology

Volumn 3, Issue FEB, 2012, Pages

  Altwasser, Robert ^a   Linde, Jörg ^a   Buyko, Ekaterina ^b   Hahn, Udo ^b   Guthke, Reinhard ^a  

^a HANS KNÖLL INSTITUTE   (Germany)

^b FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

Author keywords

Candida albicans; Hubs; LASSO; Linear regression; Network inference; Prior knowledge; Reverse engineering; Scale free

Indexed keywords

EID: 84865294429     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2012.00051     Document Type: Article

References (34)

1. Arnaud, M. B., Costanzo, M. C., Skrzypek, M. S., Shah, P., Bink-ley, G., Lane, C., Miyasato, S. R., and G, S. (2010). Candida Genome Database. Available at: http://www.candidagenome.org/
2. Barabási,A.-L.,and Oltvai,Z.N. (2004). Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5, 101-113.
3. Buyko, E., Faessler, E., Wermter, J., and Hahn, U. (2011). Syntactic simplification and semantic enrichment - trimming dependency graphs for event extraction. Comput. Intell. 27, 610-644.
4. D'Enfert, C., and Hube, B. (2007). Candida: Comparative and Functional Genomics. Norfolk: Caister Academic Press.
5. Edgar, R., Domrachev, M., and Lash, A. E. (2002). Gene expression omnibus: Ncbi gene expression and hybridization array data repository. Nucleic Acids Res. 30,207-210.
6. Faith, J. J., Hayete, B., Thaden, J. T., Mogno, I., Wierzbowski, J., Cottarel, G., Kasif, S., Collins, J. J., and Gardner, T. S. (2007). Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol. 5, e8. doi:10.1371/journal.pbio.0050008
7. Gustafsson, M., Hörnquist, M., and Lombardi, A. (2004). Large-scale reverse engineering by the lasso. Available at: http://arxiv.org/abs/q-bio/0403012v1
8. Gustafsson, M., Hörnquist, M., and Lombardi, A. (2005). Constructing and analyzing a large-scale gene-to-gene regulatory network lasso-constrained inference and biological validation. IEEE/ACM Trans. Comput. Biol. Bioinform. 2, 254-261.
9. Guthke, R., Kniemeyer, O., Albrecht, D., Brakhage, A. A., and Möller, U. (2007). Discovery of gene regulatory networks in Aspergillus fumi-gatus. Lect. Notes Bioinform. 4366, 22-41.
10. Guthke, R., Möller, U., Hoffmann, M., Thies, F., and Toepfer, S. (2005). Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection. Bioinformatics 21, 1626-1634.
11. Han, J.-D. J., Bertin, N., Hao, T., Goldberg, D. S., Berriz, G. F., Zhang, L. V., Dupuy, D., Walhout, A. J. M., Cusick, M. E., Roth, F. P., and Vidal, M. (2004). Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430, 88-93.
12. He, X., and Zhang, J. (2006). Why do hubs tend to be essential in protein networks? PLoS Genet. 2, e88. doi:10.1371/journal.pgen.0020088
13. Hecker, M., Goertsches, R. H., Engel-mann, R., Thiesen, H.-J., and Guthke, R. (2009a). Integrative modeling of transcriptional regulation in response to antirheumatic therapy. BMC Bioinformatics 10, 262. doi:10.1186/1471-2105-10-262
14. Hecker, M., Lambeck, S., Toepfer, S., van Someren, E., and Guthke, R. (2009b). Gene regulatory network inference: data integration in dynamic models - a review. BioSys-tems 96, 86-103.
15. Hube, B. (2004). From commensal to pathogen: stage- and tissue-specific gene expression of Candida albicans. Curr. Opin. Microbiol. 7, 336-341.
16. Ihmels, J., Bergmann, S., Berman, J., and Barkai, N. (2005). Comparative gene expression analysis by a differential clustering approach: application to the Candida albicans transcription program. PLoS Genet. 1, e39. doi:10.1371/journal.pgen.0010039
17. Johnston, M. (1987). A model fungal gene regulatory mechanism: the gal genes of Saccharomyces cerevisiae. Microbiol. Rev. 51, 458-476.
18. Kim, J.-D., Ohta, T., Pyysalo, S., Kano, Y., and Tsujii, J. (2011). Extracting bio-molecular events from literature the bionlp'09 shared task. Comput. Intell. 27,513-540.
19. Leclerc, R. D. (2008). Survival of the sparsest: robust gene networks are parsimonious. Mol. Syst. Biol. 4, 213.
20. Linde, J., Buyko, E., Altwasser, R., Hahn, U., and Guthke, R. (2011). Full-Genomic Network Inference for Non-Model Organisms: A Case Study for the Fungal Pathogen Candida albicans. Paris: WASET.
21. Linde, J., Wilson, D., Hube, B., and Guthke, R. (2010). Regulatory network modelling of iron acquisition by a fungal pathogen in contact with epithelial cells. BMC Syst. Biol. 4, 148. doi:10.1186/1752-0509-4-148
22. Lohr, D., Venkov, P., and Zlatanova, J. (1995). Transcriptional regulation in the yeast gal gene family: a complex genetic network. FASEB J. 9, 777-787.
23. Margolin, A. A., Nemenman, I., Basso, K., Wiggins, C., Stolovitzky, G., Favera, R. D., and Califano, A. (2006). ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 7(Suppl. 1), S7. doi:10.1186/1471-2105-7-S1-S7
24. Meyer, P. E., Kontos, K., Lafitte, E, and Bontempi, G. (2007). Information-theoretic inference of large transcriptional regulatory networks. EURASIP J. Bioinform. Syst. Biol. 2007, 8-8.
25. R Development Core Team. (2009). R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing
26. Rokas, A., and Hittinger, C. T. (2007). Transcriptional rewiring: the proof is in the eating. Curr. Biol. 17, R626-R628.
27. Shojaie, A., and Michailidis, G. (2010). Discovering graphical granger causality using the truncating lasso penalty. Bioinformatics 26, i517-i523.
28. Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P.-L., and Ideker, T. (2011). Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27, 431-432.
29. Stacklies, W., Redestig, H., Scholz, M., Walther, D., and Selbig, J. (2007). pcaMethods - a bioconductor package providing pca methods for incomplete data. Bioinformatics 23, 1164-1167.
30. Tibshirani, R. (1994). Regression shrinkage and selection via the lasso. J. R. Stat. Soc. B 58,267-288.
31. Van Rijsbergen, C. (1979). Information Retrieval, 2nd edn. London: Butter-worths.
32. Wilson, L. S., Reyes, C. M., Stolp-man, M., Speckman, J., Allen, K., and Beney, J. (2002). The direct cost and incidence of systemic fungal infections. Value Health 5, 26-34.
33. Yeung, M. K. S., Tegnr, J., and Collins, J. J. (2002). Reverse engineering gene networks using singular value decomposition and robust regression. Proc. Natl. Acad. Sci. U.S.A. 99, 6163-6168.
34. Zou, H. (2006). The adaptive lasso and its oracle properties. J. Am. Stat. Assoc. 101,1418-1429.