The OncoFinder algorithm for minimizing the errors introduced by the high-throughput methods of transcriptome analysis

Frontiers in Molecular Biosciences

Volumn 1, Issue AUG, 2014, Pages

  Buzdin, Anton A ^a,b,c   Zhavoronkov, Alex A ^b,c   Korzinkin, Mikhail B ^c,d   Roumiantsev, Sergey A ^b   Aliper, Alexander M ^b,c   Venkova, Larisa S ^c,d   Smirnov, Philip Y ^c,d   Borisov, Nikolay M ^c,d  

^a SHEMYAKIN OVCHINNIKOV INSTITUTE OF BIOORGANIC CHEMISTRY   (Russian Federation)

^b Clinical Center of Pediatric Hematology Oncology and Immunology   (Russian Federation)

^c Pathway Pharmaceuticals Limited   (Hong Kong)

^d INSTITUTE OF BIOPHYSICS   (Russian Federation)

Author keywords

Correction of errors; Gene expression; Intracellular signaling pathway activation; Microarray hybridization; Next generation sequencing; RNA Seq; Signalome; Transcriptome profiling

Indexed keywords

EID: 84920927962     PISSN: None     EISSN: 2296889X     Source Type: Journal    
DOI: 10.3389/fmolb.2014.00008     Document Type: Article

References (26)

1. Bauer-Mehren, A., Furlong, L. I., and Sanz, F. (2009). Pathway databases and tools for their exploitation: benefits, current limitations and challenges. Mol. Syst. Biol. 5:290. doi: 10.1038/msb.2009.47
2. Blagosklonny, M. V. (2012). Rapalogs in cancer prevention. Cancer Biol. Ther. 13, 1349-1354. doi: 10.4161/cbt.22859
3. Blagosklonny, M. V. (2013). Selective anti-cancer agents as anti-aging drugs. Cancer Biol. Ther. 14:1092. doi: 10.4161/cbt.27350
4. Blagosklonny, M. V., and Campisi, J. (2008). Cancer and aging. Cell Cycle 7, 2615-2618. doi: 10.4161/cc.7.17.6626
5. Bolstad, B. M., Irizarry, R. A., Astrand, M., and Speed, T. P. (2003). A comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics 19, 185-193. doi: 10.1093/bioinformatics/19.2.185
6. Buzdin, A. A., and Lukyanov, S. A. (eds.). (2007). Nucleic acids Hybridization Modern Applications. Dordrecht: Springer. ISBN: 978-1-4020-6039-7 (Print) 978-1-4020-6040-3
7. Buzdin, A. A., Zhavoronkov, A. A., Korzinkin, M. B., Venkova, L. S., Zenin, A. A., Smirnov, P. H., et al. (2014). OncoFinder, a new method for the analysis of intracellular signaling pathway activation using transcriptomic data. Front. Genet. 5, 55. doi: 10.3389/fgene.2014.00055
8. Chalaya, T., Gogvadze, E., Buzdin, A., Kovalskaya, E., and Sverdlov, E. D. (2004). Improving specificity of DNA hybridization-based methods. Nucleic Acids Res. 32:e130. doi: 10.1093/nar/gnh125
9. Elkon, R., Vesterman, R., and Amit, N. (2008). SPIKE-a database, visualization and analysis tool of cellular signaling pathways. BMC Bioinformatics 9:110. doi: 10.1093/nar/gkq1167
10. Hanahan, D., and Weinberg, R. A. (2000). The hallmarks of cancer. Cell 100, 57-70. doi: 10.1016/S0092-8674(00)81683-9
11. Haw, R., and Stein, L. (2012). Using the reactome database. Curr. Protoc. Bioinformatics. chapter 8, Unit 8.7. doi: 10.1002/0471250953.bi0807s38
12. Kholodenko, B. N., Demin, O. V., Moehren, G., and Hoek, J. B. (1999). Quantification of short term signaling by the epidermal growth factor receptor. J. Biol. Chem., 274, 30169-30181. doi: 10.1074/jbc.274.42.30169
13. Kim, S. C., Jung, Y., Park, J., Cho, S., Seo, C., Kim, J., et al. (2013). A high-dimensional, deep-sequencing study of lung adenocarcinoma in female never-smokers. PLoS ONE 8:e55596. doi: 10.1371/journal.pone.0055596
14. Kuzmina, N. B., and Borisov, N. M. (2011). Handling complex rule-based models of mitogenic cell signaling (On the example of ERK activation upon EGF stimulation). Intl. Proc. Chem. Biol. Environ. Eng. 5, 76-82
15. Mathivanan, S., Periaswamy, B., Gandhi, T., Kandasamy, K., Suresh, S., Mohmood, R., et al. (2006). An evaluation of human protein-protein interaction data in the public domain. BMC Bioinformatics 7:S19. doi: 10.1186/1471-2105-7-S5-S19
16. Moskalev, A. A., Aliper, A. M., Smit-McBride, Z., Buzdin, A., and Zhavoronkov, A. (2014). Genetics and epigenetics of aging and longevity. Cell Cycle 13, 1063-1077. doi: 10.4161/cc.28433
17. Nakaya, A., Katayama, T., Itoh, M., Hiranuka, K., Kawashima, S., Moriya, Y., et al. (2013). KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. Nucleic Acids Res. 41, D353-D357. doi: 10.1093/nar/gks1239
18. Nikitin, A., Egorov, S., Daraselia, N., and Mazo, I. (2003). Pathway studio-the analysis and navigation of molecular networks. Bioinformatics 19, 2155-2157. doi: 10.1093/bioinformatics/btg290
19. Shugay, M., Britanova, O. V., Merzlyak, E. M., Turchaninova, M. A., Mamedov, I. Z., Tuganbaev, T. R., et al. (2014). Towards error-free profiling of immune repertoires. Nat. Methods 6, 653-655. doi: 10.1038/nmeth.2960
20. Spirin, P. V., Lebedev, T. D., Orlova, N. N., Gornostaeva, A. S., Prokofjeva, M. M., Nikitenko, N. A., et al. (2014). Silencing AML1-ETO gene expression leads to simultaneous activation of both pro-apoptotic and proliferation signaling. Leukemia. doi: 10.1038/leu.2014.130. [Epub ahead of print]
21. van Delft, J., Gaj, S., Lienhard, J., Albrecht, M. W., Kirpiy, A., Brauers, M., et al. (2012). RNA-seq provides new insights in the transcriptome responses induced by the carcinogen benzo[a]pyrene. Toxicol. Sci. 130, 427-439. doi: 10.1093/toxsci/kfs250
22. Vishnyakova, K. S., Babizhayev, M. A., Aliper, A. M., Busdin, A. A., Kudryavzeva, A. V., and Yegorov, Y. E. (in press). Stimulation of proliferation by carnosine: cellular and transcriptome approaches. Mol. Biol. (Moscow)
23. Xu, X., Zhang, Y., Williams, J., Antoniou, E., McCombie, W. R., and Wu, S. (2013). Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets. BMC Bioinformatics 14(Suppl. 9):S1. doi: 10.1186/1471-2105-14-S9-S1
24. Yizhak, K., Gabay, O., Cohen, H., and Rupin, E. (2013). Model-based identification of drug targets that, revert disrupted metabolism and its application to ageing. Nat. Commun. 4:2632. doi: 10.1038/ncomms3632
25. Zhavoronkov, A., Buzdin, A. A., Garazha, A. V., Borisov, N. M., and Moskalev, A. A. (2014). Signaling pathway cloud regulation for in silico screening and ranking of the potential geroprotective drugs. Front. Genet. 5:49. doi: 10.3389/fgene.2014.00049
26. Zhavoronkov, A., and Cantor, C. R. (2011). Methods for structuring scientific knowledge from many areas related to aging research. PLoS ONE 6:e22597. doi: 10.1371/journal.pone.0022597