TutorialsNo Access

VOLCANO PLOTS IN ANALYZING DIFFERENTIAL EXPRESSIONS WITH mRNA MICROARRAYS

WENTIAN LI

The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, 350 Community Drive, NY 11030, USA

Search for more papers by this author

https://doi.org/10.1142/S0219720012310038Cited by:138 (Source: Crossref)

Abstract

A volcano plot displays unstandardized signal (e.g. log-fold-change) against noise-adjusted/standardized signal (e.g. t-statistic or -log₁₀(p-value) from the t-test). We review the basic and interactive use of the volcano plot and its crucial role in understanding the regularized t-statistic. The joint filtering gene selection criterion based on regularized statistics has a curved discriminant line in the volcano plot, as compared to the two perpendicular lines for the "double filtering" criterion. This review attempts to provide a unifying framework for discussions on alternative measures of differential expression, improved methods for estimating variance, and visual display of a microarray analysis result. We also discuss the possibility of applying volcano plots to other fields beyond microarray.

Keywords:

References

M. Schenaet al., Trends. Biotechnol. 16, 301 (1998). Crossref, Medline, Google Scholar
R. A. Young, Cell 102, 9 (2000). Crossref, Medline, Google Scholar
A. Butte, Nat. Rev. Drug. Discov. 1, 951 (2002). Crossref, Medline, Google Scholar
D. K. Slonim, Nat. Genet. 32, 502 (2002). Crossref, Medline, Google Scholar
R. B. Stoughton, Ann. Rev. Biochem. 74, 53 (2005). Crossref, Medline, Google Scholar
V. Trevino, F. Falciani and H. A. Barrera-Saldana, Mol. Med. 13, 527 (2007). Crossref, Medline, Google Scholar
A. J. Trachtenberget al., Meth. Mol. Biol. 802, 3 (2012). Crossref, Medline, Google Scholar
W. Etienneet al., BioTechniques 36, 618 (2004). Crossref, Medline, Google Scholar
P. B. Dallaset al., BMC Genomics 6, 59 (2005). Crossref, Medline, Google Scholar
J. S. Morey, J. C. Ryan and F. M. van Dolah, Biol. Proced. Online. 8, 175 (2006). Crossref, Medline, Google Scholar
P. J. Parket al., J. Biotechnol. 112, 225 (2004). Crossref, Medline, Google Scholar
J. E. Larkinet al., Nat. Meth. 2, 337 (2005). Crossref, Medline, Google Scholar
R. A. Irizarryet al., Nat. Meth. 2, 345 (2005). Crossref, Medline, Google Scholar
S. Draghiciet al., Trends. Genet. 22, 101 (2006). Crossref, Medline, Google Scholar
W. P. Kuoet al., Nat. Biotechnol. 24, 832 (2006). Crossref, Medline, Google Scholar
T. A. Pattersonet al., Nat. Biotechnol. 24, 1140 (2006). Crossref, Medline, Google Scholar
J. J. Chenet al., BMC Bioinformatics 8, 412 (2007). Crossref, Medline, Google Scholar
Z. Wenet al., Handbook of Statistical Bioinformatics, eds. H. Horng-Shing, B. Schölkopf and H. Zhao (Springer-Verlag, Berlin, Heidelberg, 2011) pp. 171–192. Crossref, Google Scholar
Z. Li, J. C. Kwekel and T. Chen, Meth. Mol. Biol. 802, 123 (2012). Crossref, Medline, Google Scholar
J. D. Allenet al., Brief Bioinform. 13, 547 (2012). Crossref, Medline, Google Scholar
G. A. Churchill, Nat. Genet. 32, 490 (2002). Crossref, Medline, Google Scholar
C. Li and A. Rabinovic, Biostatistics 8, 118 (2007). Medline, Google Scholar
K. A. Baggerly, K. R. Coombes and E. S. Neeley, J. Clin. Oncol. 26, 1186 (2008). Crossref, Medline, Google Scholar
R. R. Kitchenet al., BMC Genomics 11, 134 (2010). Crossref, Medline, Google Scholar
C. Chenet al., PLoS ONE 6, e17238 (2011). Crossref, Medline, Google Scholar
J. A. Gagnon-Bartsch and T. P. Speed, Biostatistics 13, 539 (2012). Crossref, Medline, Google Scholar
J. P. A. Ioannidis, Lancet 365, 454 (2005). Crossref, Medline, Google Scholar
J. M. Raser and E. K. O'Shea, Science 309, 2010 (2005). Crossref, Medline, Google Scholar
L. Ein-Dor, O. Zuk and E. Domany, Proc. Nat. Acad. Sci. 103, 5923 (2006). Crossref, Medline, Google Scholar
N. Maheshri and E. K. O'Shea, Annu. Rev. Biophy. Biomol. Struct. 36, 413 (2007). Crossref, Medline, Google Scholar
A. Zeiselet al., BMC Bioinformatics 11, 400 (2010). Crossref, Medline, Google Scholar
R. Thomaset al., BMC Bioinformatics 11, 576 (2010). Crossref, Medline, Google Scholar
R. R. Kitchenet al., BMC Genomics 12, 589 (2011). Crossref, Medline, Google Scholar
A. Posekany, K. Felsenstein and P. Sykacek, Bioinformatics 27, 807 (2011). Crossref, Medline, Google Scholar
V. T. Y. Tang and H. Yan, Int. J. Mach. Learn & Cyber 3, 51 (2012). Crossref, Google Scholar
V. Sharovet al., BMC Biotechnol. 4, 3 (2004). Crossref, Medline, Google Scholar
Y. H. Yang and T. Speed, Nat. Rev. Genet. 3, 579 (2002). Crossref, Medline, Google Scholar
L. Shiet al., Expert. Rev. Mol. Diagn. 4, 761 (2004). Crossref, Medline, Google Scholar
L. Shiet al., Nat. Biotechnol. 24, 1151 (2006). Crossref, Medline, Google Scholar
M. N. McCallet al., BMC Bioinformatics 12, 137 (2011). Crossref, Medline, Google Scholar
A. Brazmaet al., Nat. Genet. 29, 365 (2001). Crossref, Medline, Google Scholar
J. P. A. Ioannidiset al., Nat. Genet. 41, 149 (2009). Crossref, Medline, Google Scholar
J. Quackenbush, Nat. Genet. 32, 496 (2002). Crossref, Medline, Google Scholar
J. Vandesompeleet al., Genome. Biol. 3, 34 (2002). Google Scholar
A. Fujitaet al., BMC Bioinformatics 7, 469 (2006). Crossref, Medline, Google Scholar
C. Steinhoff and M. Vingron, Brief. Bioinform. 7, 166 (2006). Crossref, Medline, Google Scholar
P. Stafford (ed.) , Methods in Microarray Normalization ( CRC Press , Boca Raton, FL , 2008 ) . Crossref, Google Scholar
R. Autio et al. , BMC. Bioinform. 10 ( ) , S24 . Crossref, Medline, Google Scholar
J. Önskoget al., BMC. Bioinform. 12, 390 (2011). Crossref, Medline, Google Scholar
Halpert RL, Sanga S, Robust unattended microarray analysis, Ingenuity Technical Report No. 2011-1, Ingenuity Systems, Inc., 2012 . Google Scholar
K. Estradaet al., Bioinformatics 25, 2750 (2009). Crossref, Medline, Google Scholar
E. E. Schadtet al., Nat. Rev. Genet. 11, 647 (2010). Crossref, Medline, Google Scholar
T. Hastie , R. Tibshirani and J. Friedman , The Elements of Statistical Learning ( Springer , Berlin , 2001 ) . Crossref, Google Scholar
J. D. Storey and R. Tibshirani, Proc. Nat. Acad. Sci. 100, 9440 (2003). Crossref, Medline, Google Scholar
J. D. Storey, Ann. Stat. 31, 2013 (2003). Crossref, Google Scholar
A. Reiner, D. Yekutieli and Y. Benjamini, Bioinformatics 19, 368 (2003). Crossref, Medline, Google Scholar
Y. Pawitanet al., Bioinformatics 21, 3017 (2005). Crossref, Medline, Google Scholar
A. Schwwartzman and X. Lin, Biometrika 98, 199 (2011). Crossref, Medline, Google Scholar
E. P. Xing, M. I. Jordan and R. M. Karp, Feature selection for high-dimensional genomic microarray data, Proc. Eighteenth Int. Conf. Machine Learning (ICML 2001), eds. C. E. Brodley and A. P. Danyluk (Morgan Kauffmann, 2001) pp. 601–608. Google Scholar
W. Li and Y. Yang, Methods of Microarray Data Analysis, eds. S. M. Lin and K. F. Johnson (Kluwer Academic, Dordrecht, The Netherlands, 2002) pp. 137–150. Crossref, Google Scholar
C. Ambroise and G. J. McLachlan, Proc. Nat. Acad. Sci. 99, 6562 (2002). Crossref, Medline, Google Scholar
I. Guyon and A. Elisseeff, J. Mach. Learn. Res. 3, 1157 (2003). Google Scholar
H. Peng, F. Long and C. Ding, IEEE. Trans. Pattern. Anal. Mach. Learn. 27, 1226 (2005). Crossref, Medline, Google Scholar
W. Li, Bioinformatics 22, 2187 (2006). Crossref, Medline, Google Scholar
J. G. Liao and K. V. Chin, Bioinformatics 23, 1945 (2007). Crossref, Medline, Google Scholar
C. Zhaoet al., Cancer. Inform. 9, 49 (2010). Medline, Google Scholar
T. R. Golubet al., Science 286, 531 (1999). Crossref, Medline, Google Scholar
I. Hedenfalket al., New. Engl. J. Med. 344, 539 (2001). Crossref, Medline, Google Scholar
S. M. Dhanasekaranet al., Nature 412, 822 (2001). Crossref, Medline, Google Scholar
T. R. Adibet al., Brit. J. Cancer. 90, 686 (2004). Crossref, Medline, Google Scholar
T. J. Yeatman, J. Clin. Oncol. 27, 2743 (2009). Crossref, Medline, Google Scholar
S. L. Pomeroyet al., Nature 415, 436 (2002). Crossref, Medline, Google Scholar
M. J. van de Vijveret al., New. Engl. J. Med. 347, 1999 (2002). Crossref, Medline, Google Scholar
H. Colmanet al., Neuro-Oncology 12, 49 (2010). Crossref, Medline, Google Scholar
C. Kim and S. Paik, Nat. Rev. Clin. Oncol. 7, 340 (2010). Crossref, Medline, Google Scholar
N. Jainet al., Bioinformatics 19, 1945 (2003). Crossref, Medline, Google Scholar
Y. Chen, E. R. Dougherty and M. L. Bittner, J. Biomed. Opt. 2, 274 (1997). Google Scholar
P. Baldi and A. D. Long, Bioinformatics 17, 509 (2001). Crossref, Medline, Google Scholar
L. Shiet al., BMC Bioinformatics 6(), S12 (2005). Crossref, Medline, Google Scholar
L. Guoet al., Nat. Biotechnol. 24, 1162 (2006). Crossref, Medline, Google Scholar
M. Zhanget al., Bioinformatics 24, 2057 (2008). Crossref, Medline, Google Scholar
M. Zhanget al., Bioinformatics 25, 1662 (2009). Crossref, Medline, Google Scholar
A. L. Boulesteix and M. Slawski, Brief. Bioinform. 10, 556 (2009). Crossref, Medline, Google Scholar
Witten DM, Tibshirani R, A comparison of fold-change and the t-statistic for microarray data analysis, Department of Statistics, Stanford University Technical Report, 2007 . Google Scholar
R. B. O'Hara and D. J. Kotze, Math. Ecol. Evol. 1, 118 (2010). Crossref, Google Scholar
G. T. Fechner , Elemente der Psychophysik ( Breitkopf und Härtel , Leipzig , 1860 ) . Google Scholar
P. L. Auer, S. Srivastava and R. W. Doerge, Brief. Bioinform. 11, 57 (2011). Google Scholar
M. D. Robinson, D. J. McCarthy and G. K. Smyth, Bioinformatics 26, 139 (2010). Crossref, Medline, Google Scholar
A. Oshlack, M. D. Robinson and M. D. Young, Genome. Biol. 11, 220 (2010). Crossref, Medline, Google Scholar
S. Anders and W. Huber, Genome. Biol. 11, R106 (2010). Crossref, Medline, Google Scholar
T. J. Hardcastle and K. A. Kelly, BMC. Bioinform. 11, 422 (2010). Crossref, Medline, Google Scholar
L. Wanget al., Bioinformatics 26, 136 (2010). Crossref, Medline, Google Scholar
J. S. Cumbieet al., PLoS ONE 6, e25279 (2011). Crossref, Medline, Google Scholar
J. Leeet al., Cancer. Inform. 10, 205 (2011). Medline, Google Scholar
Z. Chenet al., BMC. Sys. Biol. 5(), S1 (2011). Crossref, Medline, Google Scholar
S. Tarazonaet al., Genome. Res. 21, 2213 (2011). Crossref, Medline, Google Scholar
D. M. Witten, Ann. Appl. Stat. 5, 2493 (2011). Crossref, Google Scholar
V. M. Kvam, P. Liu and Y. Si, Am. J. Botany. 99, 248 (2012). Crossref, Medline, Google Scholar
J. Liet al., Biostatistics 13, 523 (2010). Crossref, Medline, Google Scholar
G. W. Snedecor and W. G. Cochran, Statistical Methods, 8th edn. (Iowa State University Press, Ames, IW, 1989). Google Scholar
B. L. Welsh, Biometrika 34, 28 (1947). Medline, Google Scholar
J. Cohen , Statistical Power Analysis for the Behavioral Sciences , 2nd edn. ( Lawrence Erlbaum Associates Inc. , Hillsdale, NJ , 1988 ) . Google Scholar
Y. Tu, G. Stolovitzky and U. Klein, Proc. Nat. Acad. Sci. 99, 14031 (2002). Crossref, Medline, Google Scholar
X. Cui and G. A. Churchill, Genome. Biol. 4, 210 (2003). Crossref, Medline, Google Scholar
W. Jinet al., Nat. Genet. 29, 389 (2001). Crossref, Medline, Google Scholar
W. G. Alvordet al., Brief. Bioinform. 8, 1 (2007). Google Scholar
W. Pan, Bioinformatics 18, 546 (2002). Crossref, Medline, Google Scholar
S. Zhang and J. Cao, BMC Bioinformatics 10, 402 (2009). Crossref, Medline, Google Scholar
J. T. Leeket al., Nat. Rev. Genet. 11, 733 (2010). Crossref, Medline, Google Scholar
Z. Chenet al., BMC Genomics 12(), S7 (2011). Medline, Google Scholar
I. Dozmorov and I. Lefkovits, Nucleic. Acids. Res. 37, 6323 (2009). Crossref, Medline, Google Scholar
U. M. Braga-Neto and E. R. Dougherty, Bioinformatics 20, 374 (2004). Crossref, Medline, Google Scholar
X. Cuiet al., Biostatistics 6, 59 (2005). Crossref, Medline, Google Scholar
G. W. Wright and R. M. Simon, Bioinformatics 19, 2448 (2003). Crossref, Medline, Google Scholar
V. G. Tusher, R. Tibshirani and G. Chu, Proc. Nat. Acad. Sci. 98, 5116 (2001). Crossref, Medline, Google Scholar
Chu G, Narasimhan B, Tibshirani R, Tusher V, SAM: Significance Analysis of Microarrays, Users Guide and Technical Document, v.3.0, 2007. URL: http://www-stat.stanford.edu/∼tibs/SAM/sam.pdf . Google Scholar
H. Schwender, A. Krause and K. Ickstadt, RNews 6, 45 (2006). Google Scholar
B. Efronet al., J. Am. Stat. Assoc. 96, 1151 (2001). Crossref, Google Scholar
Wickham H, ggplot2: Elegant Graphics for Data Analysis, Springer, Berlin, 2009 . Google Scholar
R. C. Gentlemanet al., Genome. Biol. 5, R80 (2004). Crossref, Medline, Google Scholar
R. Gentleman et al. (eds.) , Bioinformatics and Computational Biology Solutions Using R and Bioconductor ( Springer , Berlin , 2005 ) . Crossref, Google Scholar
Y. H. Yang, Y. Xiao and M. R. Segal, Bioinformatics 21, 1084 (2005). Crossref, Medline, Google Scholar
M. Ashburneret al., Nat. Genet. 25, 25 (2000). Crossref, Medline, Google Scholar
Xiao Y, Hsiao TH, Suresh U, Chen HIH, Wu X, Wolf SE, Chen Y, A novel significance score for gene selection and ranking, Bioinformatics, to be published in 2012. doi: 10.1093/bioinformatics/btr671 . Google Scholar
W. Li, Brief. Bioinform. 9, 1 (2008). Crossref, Medline, Google Scholar
M. Sirotaet al., PLoS. Genet. 5, e1000792 (2009). Crossref, Medline, Google Scholar
K. Miclauset al., Pharmacogenom. J. 10, 324 (2010). Crossref, Medline, Google Scholar
M. B. Eisenet al., Proc. Nat. Acad. Sci. 95, 14863 (1998). Crossref, Medline, Google Scholar
Y. H. Yanget al., Nucleic. Acids. Res. 30, e15 (2002). Crossref, Medline, Google Scholar
M. Benitoet al., Bioinformatics 20, 105 (2004). Crossref, Medline, Google Scholar
H. Göhlmann and W. Talloen , Gene Expression Studies Using Affymetrix Microarrays ( Chapman & Hall/CRC , Boca Raton, FL , 2009 ) . Crossref, Google Scholar
I. Dozmorov and M. Centola, Bioinformatics 19, 204 (2003). Crossref, Medline, Google Scholar
G. K. Smyth, Stat. Appl. Genet. Mol. Biol. 3, 3 (2004). Google Scholar
H. Wuet al., The Analysis of Gene Expression Data Methods and Software, eds. G. Parmigianiet al. (Springer, Berlin, 2003) pp. 313–341. Crossref, Google Scholar
N. Dean and A. E. Raftery, BMC Bioinformatics 6, 173 (2005). Crossref, Medline, Google Scholar
Y. Linet al., The Analysis of Gene Expression Data Methods and Software, eds. G. Parmigianiet al. (Springer, Berlin, 2003) pp. 291–312. Crossref, Google Scholar
N. Pavelkaet al., BMC Bioinformatics 5, 203 (2004). Crossref, Medline, Google Scholar
H. Choet al., Proteomics 7, 3681 (2007). Crossref, Medline, Google Scholar
Åstrand M, Normalization and differential gene expression analysis of microarray data, Ph.D. Thesis, Department of Mathematics, Chalmers University of Technology and Göteborg University, 2008 . Google Scholar
R. D. Pearsonet al., BMC Bioinformatics 10, 211 (2009). Crossref, Medline, Google Scholar
R. Breitlinget al., FEBS. Lett. 573, 83 (2004). Crossref, Medline, Google Scholar
P. Broberg, Genome. Biol. 4, R41 (2004). Crossref, Medline, Google Scholar
R. B. Scharpfet al., J. Am. Stat. Assoc. 104, 1295 (2009). Crossref, Medline, Google Scholar