1,420
Views
19
CrossRef citations to date
0
Altmetric
Report

MiRImpact, a new bioinformatic method using complete microRNA expression profiles to assess their overall influence on the activity of intracellular molecular pathways

, , , , , , , , , , & show all
Pages 689-698 | Received 14 Oct 2015, Accepted 20 Jan 2016, Published online: 30 Mar 2016

References

  • Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004; 0:281-97; PMID:14744438; http://dx.doi.org/10.1016/S0092-8674(04)00045-5
  • Denli AM, Tops BBJ, Plasterk RHA, Ketting RF, Hannon GJ. Processing of primary microRNAs by the Microprocessor complex. Nature 2004; 432:231-5; PMID:15531879; http://dx.doi.org/10.1038/nature03049
  • Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993; 75:843-54; PMID:8252621; http://dx.doi.org/10.1016/0092-8674(93)90529-Y
  • Van Rooij E, Sutherland LB, Qi X, Richardson JA, Hill J, Olson EN. Control of stress-dependent cardiac growth and gene expression by a microRNA. Science 2007; 316:575-9; PMID:17379774; http://dx.doi.org/10.1126/science.1139089
  • Xiao C, Calado DP, Galler G, Thai T-H, Patterson HC, Wang J, Rajewsky N, Bender TP, Rajewsky K. MiR-150 controls B cell differentiation by targeting the transcription factor c-Myb. Cell 2007; 131:146-59; PMID:17923094; http://dx.doi.org/10.1016/j.cell.2007.07.021
  • Calin GA, Ferracin M, Cimmino A, Di Leva G, Shimizu M, Wojcik SE, Iorio M V, Visone R, Sever NI, Fabbri M, et al. A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Engl J Med 2005; 353:1793-801; PMID:16251535; http://dx.doi.org/10.1056/NEJMoa050995
  • Zabolotneva A, Tkachev V, Filatov F, Buzdin A. How many antiviral small interfering RNAs may be encoded by the mammalian genomes? Biol Direct 2010; 5:62; PMID:21059241; http://dx.doi.org/10.1186/1745-6150-5-62
  • Hsu S-D, Tseng Y-T, Shrestha S, Lin Y-L, Khaleel A, Chou C-H, Chu C-F, Huang H-Y, Lin C-M, Ho S-Y, et al. miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Res 2014; 42:D78-85; PMID:24304892; http://dx.doi.org/10.1093/nar/gkt1266
  • Vergoulis T, Vlachos IS, Alexiou P, Georgakilas G, Maragkakis M, Reczko M, Gerangelos S, Koziris N, Dalamagas T, Hatzigeorgiou AG. TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Res 2012; 40:D222-9; PMID:22135297; http://dx.doi.org/10.1093/nar/gkr1161
  • Buzdin AA, Zhavoronkov AA, Korzinkin MB, Venkova LS, Zenin AA, Smirnov PY, Borisov NM. Oncofinder, a new method for the analysis of intracellular signaling pathway activation using transcriptomic data. Front Genet 2014; 5:55; PMID:24723936; http://dx.doi.org/10.3389/fgene.2014.00055
  • Borisov NM, Terekhanova NV, Aliper AM, Venkova LS, Smirnov PY, Roumiantsev S, Korzinkin MB, Zhavoronkov AA, Buzdin AA. Signaling pathways activation profiles make better markers of cancer than expression of individual genes. Oncotarget 2014; 5:10198-205; PMID:25415353; http://dx.doi.org/10.18632/oncotarget.2548
  • Khatri P, Sirota M, Butte AJ. Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol 2012; 8:e1002375; PMID:22383865; http://dx.doi.org/10.1371/journal.pcbi.1002375
  • Khatri P, Drăghici S. Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 2005; 21:3587-95; PMID:15994189; http://dx.doi.org/10.1093/bioinformatics/bti565
  • Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, Park PJ. Discovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci U S A 2005; 102:13544-9; PMID:16174746; http://dx.doi.org/10.1073/pnas.0506577102
  • Mitrea C, Taghavi Z, Bokanizad B, Hanoudi S, Tagett R, Donato M, Voichiţa C, Drăghici S. Methods and approaches in the topology-based analysis of biological pathways. Front Physiol 2013; 4:278; PMID:24133454; http://dx.doi.org/10.3389/fphys.2013.00278
  • Afsari B, Geman D. Learning dysregulated pathways in cancers from differential variability analysis. Cancer Inform 2014; 13:61; PMID:25392694
  • Ho JWK, Stefani M, dos Remedios CG, Charleston MA. Differential variability analysis of gene expression and its application to human diseases. Bioinformatics 2008; 24:i390-8; PMID:18586739; http://dx.doi.org/10.1093/bioinformatics/btn142
  • Eddy JA, Hood L, Price ND, Geman D. Identifying tightly regulated and variably expressed networks by Differential Rank Conservation (DIRAC). PLoS Comput Biol 2010; 6:e1000792; PMID:20523739; http://dx.doi.org/10.1371/journal.pcbi.1000792
  • Buzdin AA, Zhavoronkov AA, Korzinkin MB, Roumiantsev SA, Aliper AM, Venkova LS, Smirnov PY, Borisov NM. The OncoFinder algorithm for minimizing the errors introduced by the high-throughput methods of transcriptome analysis. Front Mol Biosci 2014; 1:8; PMID:25988149; http://dx.doi.org/10.3389/fmolb.2014.00008
  • Makarev E, Fortney K, Litovchenko M, Braunewell KH, Zhavoronkov A, Atala A. Quantifying signaling pathway activation to monitor the quality of induced pluripotent stem cells. Oncotarget 2015; 6:23204-12; PMID:26327604; http://dx.doi.org/10.18632/oncotarget.4673
  • Lezhnina K, Kovalchuk O, Zhavoronkov AA, Korzinkin MB, Zabolotneva AA, Shegay P V, Sokov DG, Gaifullin NM, Rusakov IG, Aliper AM, et al. Novel robust biomarkers for human bladder cancer based on activation of intracellular signaling pathways. Oncotarget 2014; 5:9022-32; PMID:25296972; http://dx.doi.org/10.18632/oncotarget.2493
  • Spirin PV, Lebedev TD, Orlova NN, Gornostaeva AS, Prokofjeva MM, Nikitenko NA, Dmitriev SE, Buzdin AA, Borisov NM, Aliper AM, et al. Silencing AML1-ETO gene expression leads to simultaneous activation of both pro-apoptotic and proliferation signaling. Leukemia 2014; 28:2222-8; PMID:24727677; http://dx.doi.org/10.1038/leu.2014.130
  • Aliper AM, Frieden-Korovkina VP, Buzdin A, Roumiantsev SA, Zhavoronkov A. Interactome analysis of myeloid-derived suppressor cells in murine models of colon and breast cancer. Oncotarget 2014; 5:11345-53; PMID:25294811; http://dx.doi.org/10.18632/oncotarget.2489
  • Aliper AM, Csoka AB, Buzdin A, Jetka T, Roumiantsev S, Moskalev A, Zhavoronkov A. Signaling pathway activation drift during aging: Hutchinson-Gilford Progeria Syndrome fibroblasts are comparable to normal middle-age and old-age cells. Aging (Albany NY) 2015; 7:26-37; PMID:25587796
  • Makarev E, Cantor C, Zhavoronkov A, Buzdin A, Aliper A, Csoka AB. Pathway activation profiling reveals new insights into age-related macular degeneration and provides avenues for therapeutic interventions. Aging (Albany NY) 2014; 6:1064-75; PMID:25543336
  • Parkin DM, Bray F, Ferlay J, Pisani P. Global cancer statistics, 2002. CA Cancer J Clin 55:74-108; PMID:15761078; http://dx.doi.org/10.3322/canjclin.55.2.74
  • Kim W-J, Bae S-C. Molecular biomarkers in urothelial bladder cancer. Cancer Sci 2008; 99:646-52; PMID:18377416; http://dx.doi.org/10.1111/j.1349-7006.2008.00735.x
  • Majewski T, Lee S, Jeong J, Yoon D-S, Kram A, Kim M-S, Tuziak T, Bondaruk J, Lee S, Park W-S, et al. Understanding the development of human bladder cancer by using a whole-organ genomic mapping strategy. Lab Investig 2008; 88:694-721; PMID:18458673; http://dx.doi.org/10.1038/labinvest.2008.27
  • Sánchez-Carbayo M, Cordon-Cardo C. Applications of array technology: identification of molecular targets in bladder cancer. Br J Cancer 2003; 89:2172-7; PMID:14676790; http://dx.doi.org/10.1038/sj.bjc.6601406
  • Zabolotneva AA, Zhavoronkov A, Garazha A V, Roumiantsev SA, Buzdin AA. Characteristic patterns of microRNA expression in human bladder cancer. Front Genet 2012; 3:310; PMID:23316212; http://dx.doi.org/10.3389/fgene.2012.00310
  • Zabolotneva AA, Zhavoronkov AA, Shegay P V, Gaifullin NM, Alekseev BY, Roumiantsev SA, Garazha A V, Kovalchuk O, Aravin A, Buzdin AA. A systematic experimental evaluation of microRNA markers of human bladder cancer. Front Genet 2013; 4:247; PMID:24298280; http://dx.doi.org/10.3389/fgene.2013.00247
  • Zhavoronkov A, Buzdin AA, Garazha A V. Borisov NM, Moskalev AA. Signaling pathway cloud regulation for in silico screening and ranking of the potential geroprotective drugs. Front Genet 2014; 5:49; PMID:24624136; http://dx.doi.org/10.3389/fgene.2014.00049
  • Andreev DE, O'Connor PB, Fahey C, Kenny EM, Terenin IM, Dmitriev SE, Cormican P, Morris DW, Shatsky IN, Baranov PV. Translation of 5′ leaders is pervasive in genes resistant to eIF2 repression. Elife 2015; 4:e03971; PMID:25621764; http://dx.doi.org/10.7554/eLife.03971
  • Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009; 10:R25; PMID:19261174; http://dx.doi.org/10.1186/gb-2009-10-3-r25
  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009; 25:2078-9; PMID:19505943; http://dx.doi.org/10.1093/bioinformatics/btp352