DDGni: Dynamic delay gene-network inference from high-temporal data using gapped local alignment

Bioinformatics

Volumn 30, Issue 3, 2014, Pages 377-383

  Yalamanchili, Hari Krishna ^a,b   Yan, Bin ^c   Li, Mulin Jun ^a,b   Qin, Jing ^a,b   Zhao, Zhongying ^c   Chin, Francis Y L ^d   Wang, Junwen ^a,b  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b UNIVERSITY OF HONG KONG   (China)

^c HONG KONG BAPTIST UNIVERSITY   (Hong Kong)

^d Department of Mechanical Engineering   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ALGORITHM; ANIMAL; ARTICLE; CAENORHABDITIS ELEGANS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; METABOLISM; METHODOLOGY; YEAST;

ALGORITHMS; ANIMALS; CAENORHABDITIS ELEGANS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; TRANSCRIPTION FACTORS; YEASTS;

EID: 84893319771     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt692     Document Type: Article

References (39)

1. Aach, J. and Church, G.M. (2001) Aligning gene expression time series with time warping algorithms. Bioinformatics, 17, 495-508.
2. Abdulrehman, D., et al. (2011) YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface. Nucleic Acids Res., 39, D136-D140.
3. Altschul, S.F., et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
4. Androulakis, I.P., Yang, E. and Almon, R.R. (2007) Analysis of time-series gene expression data: methods, challenges, and opportunities. Annu. Rev. Biomed. Eng., 9, 205-228.
5. Bailey, T.L. and Gribskov, M. (2002) Estimating and evaluating the statistics of gapped local-alignment scores. J. Comput. Biol. A J. Comput. Mol. Cell Biol., 9, 575-593.
6. Baldi, P., et al. (2000) Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics, 16, 412-424.
7. Bao, Z., et al. (2006) Automated cell lineage tracing in Caenorhabditis elegans. Proc. Natl Acad. Sci. USA, 103, 2707-2712.
8. Bar-Joseph, Z. (2004) Analyzing time series gene expression data. Bioinformatics, 20, 2493-2503.
9. Bar-Joseph, Z., et al. (2003) Continuous representations of time-series gene expression data. J. Comput. Biol. A J. Comput. Mol. Cell Biol., 10, 341-356.
10. Blake, W.J., et al. (2003) Noise in eukaryotic gene expression. Nature, 422, 633-637.
11. Bratsun, D., et al. (2005) Delay-induced stochastic oscillations in gene regulation. Proc. Natl Acad. Sci. USA, 102, 14593-14598.
12. Davidson, E. and Levine, M. (2005) Gene regulatory networks. Proc. Natl Acad. Sci. USA, 102, 4935-4935.
13. Huang, T., et al. (2010) Using GeneReg to construct time delay gene regulatory networks. BMC Res. Notes, 3, 142.
14. Huynh-Thu, V.A., et al. (2010) Inferring regulatory networks from expression data using tree-based methods. PLoS One, 5, e12776.
15. Josic, K., et al. (2011) Stochastic delay accelerates signaling in gene networks. PLoS Comput. Biol., 7, e1002264.
16. Lee, C.-P., Leu, Y. and Yang, W.-N. (2012) Constructing gene regulatory networks from microarray data using GA/PSO with DTW. Applied Soft Comput., 12, 1115-1124.
17. Li, M.J., Sham, P.C. and Wang, J.W. (2010) FastPval: a fast and memory efficient program to calculate very low P-values from empirical distribution. Bioinformatics, 26, 2897-2899.
18. Madhamshettiwar, P.B., et al. (2012) Gene regulatory network inference: evaluation and application to ovarian cancer allows the prioritization of drug targets. Genome Med., 4, 41.
19. Marbach, D., et al. (2010) Revealing strengths and weaknesses of methods for gene network inference. Proc. Natl Acad. Sci. USA, 107, 6286-6291.
20. Margolin, A.A., et al. (2006) ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinform., 7 (Suppl. 1) , S7.
21. Murray, J.I., et al. (2006) The lineaging of fluorescently-labeled Caenorhabditis elegans embryos with StarryNite and AceTree. Nat. Protoc., 1, 1468-1476.
22. Murray, J.I., et al. (2008) Automated analysis of embryonic gene expression with cellular resolution in C.elegans. Nature Methods, 5, 703-709.
23. Murray, J.I., et al. (2012) Multidimensional regulation of gene expression in the Caenorhabditis elegans embryo. Genome Res., 22, 1282-1294.
24. Orlando, D.A., et al. (2008) Global control of cell-cycle transcription by coupled CDK and network oscillators. Nature, 453, 944-947.
25. Pearson, W.R. (1996) Effective protein sequence comparison. Methods Enzymol., 266, 227-258.
26. Powers, D.M.W. (2011) Evaluation: from precision, recall and F-factor to ROC, informedness, Markedness & Correlation. J. Machine Learn. Technol., 2, 37-63.
27. Prelic, A., et al. (2006) A systematic comparison and evaluation of biclustering methods for gene expression data. Bioinformatics, 22, 1122-1129.
28. Qin, J., et al. (2011) ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor. Nucleic Acids Res., 39, W430-W436.
29. Reshef, D.N., et al. (2011) Detecting novel associations in large datasets. Science, 334, 1518-1524.
30. Rhudy, M., et al. (2010) Microphone array analysis methods using cross-correlations. Imece2009, Vol 15: Sound, Vibration and Design, 281-288.
31. Riccadonna, S., et al. (2012) DTW-MIC coexpression networks from time-course data. arXiv:1210.3149 [q-bio.MN].
32. Schaffter, T., et al. (2011) GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods. Bioinformatics, 27, 2263-2270.
33. Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
34. Spellman, P.T., et al. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell, 9, 3273-3297.
35. Stolovitzky, G., et al. (2009) Lessons from the DREAM2 Challenges. Ann. New York Acad. Sci., 1158, 159-195.
36. Szklarczyk, D., et al. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res., 39, D561-D568.
37. White, K.P., et al. (1999) Microarray analysis of Drosophila development during metamorphosis. Science, 286, 2179-2184.
38. Zhu, R., et al. (2007) Studying genetic regulatory networks at the molecular level: delayed reaction stochastic models. J. Theor. Biol., 246, 725-745.
39. Zoppoli, P., et al. (2010) TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach. BMC Bioinform., 11, 154.