Full-genomic network inference for non-model organisms: A case study for the fungal pathogen Candida albicans

World Academy of Science, Engineering and Technology

Volumn 80, Issue , 2011, Pages 224-228

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

^a HANS KNÖLL INSTITUTE   (Germany)

^b FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

Author keywords

Candida albicans; LASSO; Linear regression; Modelling; Mutual information; Network inference; Pathogen; Reverse engineering; Text mining

Indexed keywords

CANDIDA ALBICANS; LASSO; MODELLING; MUTUAL INFORMATIONS; NETWORK INFERENCE; TEXT-MINING;

ACTIVE NETWORKS; BIOLOGY; CANDIDA; GENES; PATHOGENS; REVERSE ENGINEERING; YEAST; DIGITAL STORAGE; LINEAR REGRESSION; MODELS;

ARTS COMPUTING; CANDIDA;

EID: 80052162101     PISSN: 2010376X     EISSN: 20103778     Source Type: Journal    
DOI: None     Document Type: Article

References (37)

1. J. J. Faith et al., "Large-scale mapping and validation of escherichia coli transcriptional regulation from a compendium of expression profiles. " PLoS Biol, vol. 5, no. 1, p. e8, Jan 2007. [Online]. Available: http://dx.doi.org/10.1371/journal.pbio.0050008
2. R. Opgen-Rhein and K. Strimmer, "From correlation to causation networks: a simple approximate learning algorithm and its application to high-dimensional plant gene expression data. " BMC Syst Biol, vol. 1, p. 37, 2007. [Online]. Available: http://dx.doi.org/10.1186/1752-0509-1-37
3. A. A. Margolin et al., "Aracne: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. " BMC Bioinformatics, vol. 7 Suppl 1, p. S7, 2006. [Online]. Available: http://dx.doi.org/10.1186/1471-2105-7-S1-S7
4. A. J. Butte and I. S. Kohane, "Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. " Pac Symp Biocomput, pp. 418-429, 2000.
5. M. Gustafsson, M. Hörnquist, and A. Lombardi, "Constructing and analyzing a large-scale gene-to-gene regulatory network-lassoconstrained inference and biological validation. " IEEE/ACM Trans Comput Biol Bioinform, vol. 2, no. 3, pp. 254-261, 2005. [Online]. Available: http://dx.doi.org/10.1109/TCBB.2005.35
6. M. Hecker et al., "Integrative modeling of transcriptional regulation in response to antirheumatic therapy. " BMC Bioinformatics, vol. 10, p. 262, 2009. [Online]. Available: http://dx.doi.org/10.1186/1471-2105-10-262
7. M. Gustafsson, M. Hörnquist, J. Björkegren, and J. Tegnr, "Soft integration of data for reverse engineering, " in International Conference on Systems Biology,2008, 2008, pp. 127-127.
8. J. Linde, D. Wilson, B. Hube, and R. Guthke, "Regulatory network modelling of iron acquisition by a fungal pathogen in contact with epithelial cells. " BMC Syst Biol, vol. 4, no. 1, p. 148, 2010. [Online]. Available: http://dx.doi.org/10.1186/1752-0509-4-148
9. H. Yoon et al., "Coordinated regulation of virulence during systemic infection of salmonella enterica serovar typhimurium. " PLoS Pathog, vol. 5, no. 2, p. e1000306, Feb 2009. [Online]. Available: http://dx.doi.org/10.1371/journal.ppat.1000306
10. R. Guthke et al., "Discovery of gene regulatory networks in aspergillus fumigatus. " Lect Notes Bioinf, vol. 4366, pp. 22-41, 2007.
11. Y.-C. Wang et al., "Global screening of potential candida albicans biofilm-related transcription factors via network comparison. " BMC Bioinformatics, vol. 11, p. 53, 2010. [Online]. Available: http://dx.doi.org/10.1186/1471-2105-11-53
12. A. M. Huerta, H. Salgado, D. Thieffry, and J. Collado-Vides, "RegulonDB: a database on transcriptional regulation in Escherichia coli, " Nucleic Acids Res., vol. 26, no. 1, pp. 55-59, 1998.
13. R. Edgar, M. Domrachev, and A. E. Lash, "Gene expression omnibus: Ncbi gene expression and hybridization array data repository. " Nucleic Acids Res, vol. 30, no. 1, pp. 207-210, Jan 2002.
14. L. S. Wilson et al., "The direct cost and incidence of systemic fungal infections. " Value Health, vol. 5, no. 1, pp. 26-34, 2002.
15. B. Hube, "From commensal to pathogen: stage-and tissuespecific gene expression of candida albicans. " Curr Opin Microbiol, vol. 7, no. 4, pp. 336-341, Aug 2004. [Online]. Available: http://dx.doi.org/10.1016/j.mib.2004.06.003
16. K. Zakikhany et al., "In vivo transcript profiling of candida albicans identifies a gene essential for interepithelial dissemination. " Cell Microbiol, vol. 9, no. 12, pp. 2938-2954, Dec 2007. [Online]. Available: http://dx.doi.org/10.1111/j.1462-5822.2007.01009.x
17. W. A. Baumgartner(Jr.) et al., "Manual curation is not sufficient for annotation of genomic databases. " in ISMB/ECCB (Supplement of Bioinformatics), 2007, pp. 41-48.
18. U. Hahn, J. Wermter, R. Blasczyk, and P. A. Horn, "Text mining: Powering the database revolution (correspondence), " Nature, vol. 448, no. 7150, p. 130, 2007.
19. L. Hirschman, A. S. Yeh, C. Blaschke, and A. Valencia, "Overview of biocreative: Critical assessment of information extraction for biology, " BMC Bioinformatics, vol. 6, no. Supplement 1: S1, 2005.
20. J.-D. Kim et al., "Overview of BioNLP'09 Shared Task on Event Extraction, " in Proceedings BioNLP 2009. Companion Volume: Shared Task on Event Extraction. Boulder, Colorado, USA, June 4-5, 2009, 2009, pp. 1-9.
21. C. Rodríguez-Penagos, H. Salgado, I. Martínez-Flores, and J. Collado-Vides, "Automatic reconstruction of a bacterial regulatory network using natural language processing, " BMC Bioinformatics, vol. 8, no. 293, 2007. [Online]. Available: http://www.biomedcentral.com/1471-2105/8/293
22. U. Hahn et al., "How feasible and robust is the automatic extraction of gene regulation events? a cross-method evaluation under lab and real-life conditions, " in Proceedings of the NAACL workshop on BioNLP 2009. Association for Computational Linguistics, 2009, pp. 37-45.
23. D. Albrecht, O. Kniemeyer, A. A. Brakhage, and R. Guthke, "Missing values in gel-based proteomics. " Proteomics, vol. 10, no. 6, pp. 1202-1211, Mar 2010. [Online]. Available: http://dx.doi.org/10.1002/pmic.200800576
24. T. Hastie et al., "Imputing missing data for gene expression arrays, " 1999.
25. W. Stacklies et al., "pcamethods-a bioconductor package providing pca methods for incomplete data. " Bioinformatics, vol. 23, no. 9, pp. 1164-1167, May 2007. [Online]. Available: http://dx.doi.org/10.1093/bioinformatics/btm069
26. M. B. Arnaud et al., "Candida genome database, " http://www.candidagenome.org/.
27. U. Güldener et al., "MPact: the MIPS protein interaction resource on yeast, " Nucleic Acids Research, vol. 34, no. Database issue, pp. D436-441, Jan. 2006, PMID: 16381906. [Online]. Available: http://www.ncbi.nlm.nih.gov/pubmed/16381906
28. G. D. Bader, D. Betel, and C. W. V. Hogue, "Bind: the biomolecular interaction network database. " Nucleic Acids Res, vol. 31, no. 1, pp. 248-250, Jan 2003.
29. S. Balaji et al., "Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. " J Mol Biol, vol. 360, no. 1, pp. 213-227, Jun 2006. [Online]. Available: http://dx.doi.org/10.1016/j.jmb.2006.04.029
30. E. Wingender, P. Dietze, H. Karas, and R. Knüppel, "TRANSFAC: a database on transcription factors and their DNA binding sites, " Nucleic Acids Research, vol. 24, no. 1, pp. 238-241, Jan. 1996. [Online]. Available: http://nar.oxfordjournals.org/content/24/1/238.abstract
31. E. Buyko, E. Faessler, J. Wermter, and U. Hahn, "Syntactic simplification and semantic enrichment-Trimming dependency graphs for event extraction, " Computational Intelligence, in print, 2011.
32. E. Buyko, E. Faessler, J. Wermter, and U. Hahn, "Event extraction from trimmed dependency graphs, " in Proceedings BioNLP 2009. Companion Volume: Shared Task on Event Extraction. Boulder, Colorado, USA, June 4-5, 2009, 2009, pp. 19-27.
33. R. Tibshirani, "Regression shrinkage and selection via the lasso, " JOURNAL OF THE ROYAL STATISTICAL SOCIETY, SERIES B, vol. 58, pp. 267-288, 1994. [Online]. Available: http://citeseerx.ist. psu.edu/viewdoc/summary?doi=10.1.1.35.7574
34. H. Zou, "The adaptive lasso and its oracle properties, " Journal of the American Statistical Association, vol. 101, pp. 1418-1429, December 2006. [Online]. Available: http://ideas.repec.org/a/bes/jnlasa/v101y2006p1418-1429.html
35. I. J. B Efron, T Hastie and R. Tibshirani, "Least angle regression, " The Annals of Statistics, vol. 32, no. 2, pp. 407-499, 2004.
36. J. Friedman, T. Hastie, and R. Tibshirani, "Regularization paths for generalized linear models via coordinate descent, " 2009. [Online]. Available: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.149. 3333
37. G. Stolovitzky, D. Monroe, and A. Califano, "Dialogue on reverseengineering assessment and methods: the dream of high-throughput pathway inference. " Ann N Y Acad Sci, vol. 1115, pp. 1-22, Dec 2007. [Online]. Available: http://dx.doi.org/10.1196/annals.1407.021