Frequency-based time-series gene expression recomposition using PRIISM

BMC Systems Biology

Volumn 6, Issue , 2012, Pages

  Rosa, Bruce A ^a,b   Jiao, Yuhua ^b   Oh, Sookyung ^b   Montgomery, Beronda L ^b,c   Qin, Wensheng ^a   Chen, Jin ^b,d  

^a LAKEHEAD UNIVERSITY   (Canada)

^b MICHIGAN STATE UNIVERSITY   (United States)

^c Michigan State University   (United States)

^d Michigan State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS;

TRANSCRIPTOME;

ALGORITHM; ARABIDOPSIS; ARTICLE; AUTOMATED PATTERN RECOGNITION; CIRCADIAN RHYTHM; COLD; DNA MICROARRAY; FOURIER ANALYSIS; GENETICS; METHODOLOGY; PHYSIOLOGICAL STRESS; PHYSIOLOGY;

ALGORITHMS; ARABIDOPSIS; CIRCADIAN RHYTHM; COLD TEMPERATURE; FOURIER ANALYSIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PATTERN RECOGNITION, AUTOMATED; STRESS, PHYSIOLOGICAL; TRANSCRIPTOME;

EID: 84862180455     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-6-69     Document Type: Article

References (91)

1. Cui X, Churchill GA. Statistical tests for differential expression in cDNA microarray experiments. Genome Biol 2003, 4:210. 10.1186/gb-2003-4-4-210, 154570, 12702200.
2. Adams S, Carre IA. Downstream of the plant circadian clock: output pathways for the control of physiology and development. Essays Biochem 2011, 49:53-69.
3. Bilgin DD, Zavala JA, Zhu J, Clough SJ, Ort DR, DeLucia EH. Biotic stress globally downregulates photosynthesis genes. Plant Cell Environ 2010, 33:1597-1613. 10.1111/j.1365-3040.2010.02167.x, 20444224.
4. Chaves MM, Flexas J, Pinheiro C. Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell. Ann Bot 2009, 103:551-560. 2707345, 18662937.
5. Michael TP, Mockler TC, Breton G, McEntee C, Byer A, Trout JD, Hazen SP, Shen R, Priest HD, Sullivan CM, et al. Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules. PLoS Genet 2008, 4:e14. 10.1371/journal.pgen.0040014, 2222925, 18248097.
6. Bieniawska Z, Espinoza C, Schlereth A, Sulpice R, Hincha DK, Hannah MA. Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome. Plant Physiol 2008, 147:263-279. 10.1104/pp.108.118059, 2330297, 18375597.
7. Espinoza C, Degenkolbe T, Caldana C, Zuther E, Leisse A, Willmitzer L, Hincha DK, Hannah MA. Interaction with diurnal and circadian regulation results in dynamic metabolic and transcriptional changes during cold acclimation in Arabidopsis. PLoS One 2010, 5:e14101. 10.1371/journal.pone.0014101, 2990718, 21124901.
8. Nakamichi N, Kusano M, Fukushima A, Kita M, Ito S, Yamashino T, Saito K, Sakakibara H, Mizuno T. Transcript profiling of an Arabidopsis PSEUDO RESPONSE REGULATOR arrhythmic triple mutant reveals a role for the circadian clock in cold stress response. Plant Cell Physiol 2009, 50:447-462. 10.1093/pcp/pcp004, 19131357.
9. Espinoza C, Bieniawska Z, Hincha DK, Hannah MA. Interactions between the circadian clock and cold-response in Arabidopsis. Plant Signal Behav 2008, 3:593-594. 10.4161/psb.3.8.6340, 2634507, 19704808.
10. Schliep A, Steinhoff C, Schonhuth A. Robust inference of groups in gene expression time-courses using mixtures of HMMs. Bioinformatics 2004, 20(Suppl 1):i283-i289. 10.1093/bioinformatics/bth937, 15262810.
11. Verducci JS, Melfi VF, Lin S, Wang Z, Roy S, Sen CK. Microarray analysis of gene expression: considerations in data mining and statistical treatment. Physiol Genomics 2006, 25:355-363. 10.1152/physiolgenomics.00314.2004, 16554544.
12. Dejean S, Martin PG, Baccini A, Besse P. Clustering time-series gene expression data using smoothing spline derivatives. EURASIP J Bioinform Syst Biol 2007, 70561.
13. Ernst J, Nau GJ, Bar-Joseph Z. Clustering short time series gene expression data. Bioinformatics 2005, 21(Suppl 1):i159-i168. 10.1093/bioinformatics/bti1022, 15961453.
14. Hestilow TJ, Huang Y. Clustering of gene expression data based on shape similarity. EURASIP J Bioinform Syst Biol 2009, 195712.
15. Syeda-Mahmood T. Clustering time-varying gene expression profiles using scale-space signals. Proc IEEE Comput Soc Bioinform Conf 2003, 2:48-56.
16. Koenig L, Youn E. Hierarchical Signature Clustering for Time Series Microarray Data: Software Tools and Algorithms for Biological Systems Volume 696 2011, 57-65. Springer, New York.
17. Chiappetta P, Roubaud MC, Torresani B. Blind source separation and the analysis of microarray data. J Comput Biol 2004, 11:1090-1109. 10.1089/cmb.2004.11.1090, 15662200.
18. Salome PA, Xie Q, McClung CR. Circadian timekeeping during early Arabidopsis development. Plant Physiol 2008, 147:1110-1125. 10.1104/pp.108.117622, 2442538, 18480377.
19. Morker KH, Roberts MR. Light exerts multiple levels of influence on the Arabidopsis wound response. Plant Cell Environ 2011, 34:717-728. 10.1111/j.1365-3040.2011.02276.x, 21241328.
20. Dong MA, Farre EM, Thomashow MF. Circadian clock-associated 1 and late elongated hypocotyL regulate expression of the C-REPEAT BINDING FACTOR (CBF) pathway in Arabidopsis. Proc Natl Acad Sci U S A 2011, 108:7241-7246. 10.1073/pnas.1103741108, 3084081, 21471455.
21. Bar-Joseph Z, Gerber G, Simon I, Gifford DK, Jaakkola TS. Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes. Proc Natl Acad Sci U S A 2003, 100:10146-10151. 10.1073/pnas.1732547100, 193530, 12934016.
22. Edwards KD, Anderson PE, Hall A, Salathia NS, Locke JCW, Lynn JR, Straume M, Smith JQ, Millar AJ. Flowering locus C mediates natural variation in the high-temperature response of the Arabidopsis circadian clock. Plant Cell Online 2006, 18:639-650.
23. Harmer SL, Hogenesch JB, Straume M, Chang HS, Han B, Zhu T, Wang X, Kreps JA, Kay SA. Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 2000, 290:2110-2113. 10.1126/science.290.5499.2110, 11118138.
24. Ptitsyn A. Comprehensive analysis of circadian periodic pattern in plant transcriptome. Bioinforma 2008, 9:S18.
25. Price TS, Baggs JE, Curtis AM, Fitzgerald GA, Hogenesch JB. WAVECLOCK: wavelet analysis of circadian oscillation. Bioinformatics 2008, 24:2794-2795. 10.1093/bioinformatics/btn521, 2639275, 18931366.
26. Mockler TC, Michael TP, Priest HD, Shen R, Sullivan CM, Givan SA, McEntee C, Kay SA, Chory J. The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis. Cold Spring Harb Symp Quant Biol 2007, 72:353-363. 10.1101/sqb.2007.72.006, 18419293.
27. Lu Y, Rosenfeld R, Bar-Joseph Z. Identifying cycling genes by combining sequence homology and expression data. Bioinformatics 2006, 22:e314-e322. 10.1093/bioinformatics/btl229, 16873488.
28. Wichert S, Fokianos K, Strimmer K. Identifying periodically expressed transcripts in microarray time series data. Bioinformatics 2004, 20:5-20. 10.1093/bioinformatics/btg364, 14693803.
29. Rustici G, Mata J, Kivinen K, Lio P, Penkett CJ, Burns G, Hayles J, Brazma A, Nurse P, Bahler J. Periodic gene expression program of the fission yeast cell cycle. Nat Genet 2004, 36:809-817. 10.1038/ng1377, 15195092.
30. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 1998, 9:3273-3297. 25624, 9843569.
31. Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, Alexander KE, Matese JC, Perou CM, Hurt MM, Brown PO, Botstein D. Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell 2002, 13:1977-2000. 10.1091/mbc.02-02-0030., 117619, 12058064.
32. Bozdech Z, Llinás M, Pulliam BL, Wong ED, Zhu J, DeRisi JL. The Transcriptome of the Intraerythrocytic Developmental Cycle of Plasmodium falciparum. PLoS Biol 2003, 1:e5. 176545, 12929205.
33. Marks RJ. Introduction to Shannon Sampling and Interpolation Theory 1991, Springer, New York, USA.
34. Craigon DJ, James N, Okyere J, Higgins J, Jotham J, May S. NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Res 2004, 32:D575-D577. 10.1093/nar/gkh133, 308867, 14681484.
35. Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, et al. ArrayExpress update-from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res 2009, 37:D868-D872. 10.1093/nar/gkn889, 2686529, 19015125.
36. Hubble J, Demeter J, Jin H, Mao M, Nitzberg M, Reddy TB, Wymore F, Zachariah ZK, Sherlock G, Ball CA. Implementation of GenePattern within the Stanford Microarray Database. Nucleic Acids Res 2009, 37:D898-D901. 10.1093/nar/gkn786, 2686537, 18953035.
37. Oran Brigham E. The fast Fourier transform and its applications. Upper Saddle River 1988, Prentice-Hall, Inc, NJ, USA.
38. Tominaga D. Periodicity detection method for small-sample time series datasets. Bioinform Biol Insights 2010, 4:127-136. 2998870, 21151841.
39. Team RDC. R: A language and environment for statistical computing 2011, R Foundation for Statistical Computing, Vienna, Austria.
40. Inc. TM: MATLAB 2010, Natick, Massachusetts, Inc. TM: MATLAB.
41. Harmer SL. The Circadian System in Higher Plants 2009, 357-377. , Palo Alto, Annual Review of Plant Biology.
42. Nakamichi N. Molecular Mechanisms Underlying the Arabidopsis Circadian Clock. Plant Cell Physiol 2011, 52:1709-1718. 10.1093/pcp/pcr118, 3189347, 21873329.
43. Li HM, Altschmied L, Chory J. Arabidopsis mutants define downstream branches in the phototransduction pathway. Genes Dev 1994, 8:339-349. 10.1101/gad.8.3.339, 8314087.
44. Lu SX, Tobin EM. Chromatin remodeling and the circadian clock: Jumonji C-domain containing proteins. Plant Signal Behav 2011, 6:810-814. 10.4161/psb.6.6.15171, 3218477, 21617366.
45. Mas P. Circadian clock function in Arabidopsis thaliana: time beyond transcription. Trends Cell Biol 2008, 18:273-281. 10.1016/j.tcb.2008.03.005, 18468438.
46. Thines B, Harmon FG. Four easy pieces: mechanisms underlying circadian regulation of growth and development. Curr Opin Plant Biol 2011, 14:31-37. 10.1016/j.pbi.2010.09.009, 20943429.
47. Sinclair I, Dunton J. Electronic and Electrical Servicing: Consumer and commercial electronics 2007, Elsevier, Burlington, MA, 2.
48. Chatterjee P, Mukherjee S, Chaudhuri S, Seetharaman G. Application Of PapoulisGerchberg Method In Image Super-Resolution and Inpainting. Comput J 2009, 52:80-89.
49. Orfanidis S. Introduction to signal processing 1995, Prentice Hall, New Jersey, USA.
50. Fowler SG, Cook D, Thomashow MF. Low temperature induction of Arabidopsis CBF1, 2, and 3 is gated by the circadian clock. Plant Physiol 2005, 137:961-968. 10.1104/pp.104.058354, 1065397, 15728337.
51. B-h L, Henderson DA, Zhu J-K. The Arabidopsis Cold-Responsive Transcriptome and Its Regulation by ICE1. Plant Cell Online 2005, 17:3155-3175.
52. Bar-Joseph Z, Gerber GK, Gifford DK, Jaakkola TS, Simon I. Continuous representations of time-series gene expression data. J Comput Biol 2003, 10:341-356. 10.1089/10665270360688057, 12935332.
53. Smith AA, Craven M. Fast multisegment alignments for temporal expression profiles. Comput Syst Bioinformatics Conf 2008, 7:315-326. 2766602, 19642291.
54. Vogel JT, Zarka DG, Van Buskirk HA, Fowler SG, Thomashow MF. Roles of the CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis. Plant J 2005, 41:195-211.
55. Parodi S, Muselli M, Fontana V, Bonassi S. ROC curves are a suitable and flexible tool for the analysis of gene expression profiles. Cytogenet Genome Res 2003, 101:90-91. 10.1159/000074404, 14571143.
56. Raychaudhuri S, Stuart JM, Altman RB. Principal components analysis to summarize microarray experiments: application to sporulation time series. Pac Symp Biocomput 2000, 5:455-466.
57. Gilmour SJ, Zarka DG, Stockinger EJ, Salazar MP, Houghton JM, Thomashow MF. Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression. Plant J 1998, 16:433-442. 10.1046/j.1365-313x.1998.00310.x, 9881163.
58. Maruyama K, Sakuma Y, Kasuga M, Ito Y, Seki M, Goda H, Shimada Y, Yoshida S, Shinozaki K, Yamaguchi-Shinozaki K. Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems. Plant J 2004, 38:982-993. 10.1111/j.1365-313X.2004.02100.x, 15165189.
59. Fowler S, Thomashow MF. Arabidopsis Transcriptome Profiling Indicates That Multiple Regulatory Pathways Are Activated during Cold Acclimation in Addition to the CBF Cold Response Pathway. The Plant Cell Online 2002, 14:1675-1690.
60. Hundertmark M, Hincha DK. LEA (late embryogenesis abundant) proteins and their encoding genes in Arabidopsis thaliana. BMC Genomics 2008, 9:118. 10.1186/1471-2164-9-118, 2292704, 18318901.
61. Boerjan W, Ralph J, Baucher M. Lignin biosynthesis. Annu Rev Plant Biol 2003, 54:519-546.
62. Lacombe E, Hawkins S, Van Doorsselaere J, Piquemal J, Goffner D, Poeydomenge O, Boudet AM, Grima-Pettenati J. Cinnamoyl CoA reductase, the first committed enzyme of the lignin branch biosynthetic pathway: cloning, expression and phylogenetic relationships. Plant J 1997, 11:429-441. 10.1046/j.1365-313X.1997.11030429.x, 9107033.
63. Solecka D. Role of phenylpropanoid compounds in plant responses to different stress factors. Acta Physiologiae Plantarum 1997, 19:257-268.
64. Athanasiou K, Dyson BC, Webster RE, Johnson GN. Dynamic acclimation of photosynthesis increases plant fitness in changing environments. Plant Physiol 2010, 152:366-373. 10.1104/pp.109.149351, 2799370, 19939944.
65. Hannah MA, Wiese D, Freund S, Fiehn O, Heyer AG, Hincha DK. Natural genetic variation of freezing tolerance in Arabidopsis. Plant Physiol 2006, 142:98-112. 10.1104/pp.106.081141, 1557609, 16844837.
66. Onda Y, Yagi Y, Saito Y, Takenaka N, Toyoshima Y. Light induction of Arabidopsis SIG1 and SIG5 transcripts in mature leaves: differential roles of cryptochrome 1 and cryptochrome 2 and dual function of SIG5 in the recognition of plastid promoters. Plant J 2008, 55:968-978. 10.1111/j.1365-313X.2008.03567.x, 18532976.
67. Yao J, Roy-Chowdhury S, Allison LA. AtSig5 Is an Essential Nucleus-Encoded Arabidopsis σ-Like Factor. Plant Physiol 2003, 132:739-747. 10.1104/pp.102.017913, 167013, 12805603.
68. Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, et al. The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res 2008, 36:D1009-1014. 2238962, 17986450.
69. Soitamo A, Piippo M, Allahverdiyeva Y, Battchikova N, Aro E-M. Light has a specific role in modulating Arabidopsis gene expression at low temperature. BMC Plant Biology 2008, 8:13. 10.1186/1471-2229-8-13, 2253524, 18230142.
70. Ma S, Bohnert H. Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression. Genome Biol 2007, 8:R49. 10.1186/gb-2007-8-4-r49, 1896000, 17408486.
71. Xin Z, Mandaokar A, Chen J, Last RL, Browse J. Arabidopsis ESK1 encodes a novel regulator of freezing tolerance. Plant J 2007, 49:786-799. 10.1111/j.1365-313X.2006.02994.x, 17316173.
72. Katoh A, Uenohara K, Akita M, Hashimoto T. Early steps in the biosynthesis of NAD in Arabidopsis start with aspartate and occur in the plastid. Plant Physiol 2006, 141:851-857. 10.1104/pp.106.081091, 1489895, 16698895.
73. Ruiz JM, Sanchez E, Garcia PC, Lopez-Lefebre LR, Rivero RM, Romero L. Proline metabolism and NAD kinase activity in greenbean plants subjected to cold-shock. Phytochemistry 2002, 59:473-478. 10.1016/S0031-9422(01)00481-2, 11853741.
74. Vanderauwera S, Zimmermann P, Rombauts S, Vandenabeele S, Langebartels C, Gruissem W, Inzé D, Van Breusegem F. Genome-wide analysis of hydrogen peroxide-regulated gene expression in arabidopsis reveals a high light-induced transcriptional cluster involved in anthocyanin biosynthesis. Plant Physiol 2005, 139:806-821. 10.1104/pp.105.065896, 1255997, 16183842.
75. Stracke R, Ishihara H, Huep G, Barsch A, Mehrtens F, Niehaus K, Weisshaar B. Differential regulation of closely related R2R3-MYB transcription factors controls flavonol accumulation in different parts of the Arabidopsis thaliana seedling. Plant J 2007, 50:660-677. 10.1111/j.1365-313X.2007.03078.x, 1976380, 17419845.
76. Korn M, Peterek S, Mock HP, Heyer AG, Hincha DK. Heterosis in the freezing tolerance, and sugar and flavonoid contents of crosses between Arabidopsis thaliana accessions of widely varying freezing tolerance. Plant Cell Environ 2008, 31:813-827. 10.1111/j.1365-3040.2008.01800.x, 2440548, 18284584.
77. Jonassen E, Lea U, Lillo C. HY5 & HYH are positive regulators of nitrate reductase in seedlings and rosette stage plants. Planta 2008, 227:559-564. 10.1007/s00425-007-0638-4, 17929051.
78. Zhang Y, Zheng S, Liu Z, Wang L, Bi Y. Both HY5 and HYH are necessary regulators for low temperature-induced anthocyanin accumulation in Arabidopsis seedlings. J Plant Physiol 2011, 168:367-374. 10.1016/j.jplph.2010.07.025, 20932601.
79. Sappl PG, Onate-Sanchez L, Singh KB, Millar AH. Proteomic analysis of glutathione S -transferases of Arabidopsis thaliana reveals differential salicylic acid-induced expression of the plant-specific phi and tau classes. Plant Mol Biol 2004, 54:205-219.
80. Lin WH, Ye R, Ma H, Xu ZH, Xue HW. DNA chip-based expression profile analysis indicates involvement of the phosphatidylinositol signaling pathway in multiple plant responses to hormone and abiotic treatments. Cell Res 2004, 14:34-45. 10.1038/sj.cr.7290200, 15040888.
81. Vergnolle C, Vaultier M-N, Taconnat L, Renou J-P, Kader J-C, Zachowski A, Ruelland E. The cold-induced early activation of phospholipase C and D pathways determines the response of two distinct clusters of genes in arabidopsis cell suspensions. Plant Physiol 2005, 139:1217-1233. 10.1104/pp.105.068171, 1283760, 16258011.
82. Huang D, Wu W, Abrams SR, Cutler AJ. The relationship of drought-related gene expression in Arabidopsis thaliana to hormonal and environmental factors. J Exp Bot 2008, 59:2991-3007. 10.1093/jxb/ern155, 2504347, 18552355.
83. Kreps JA, Wu Y, Chang H-S, Zhu T, Wang X, Harper JF. Transcriptome changes for arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol 2002, 130:2129-2141. 10.1104/pp.008532, 166725, 12481097.
84. Tepperman JM, Hwang Y-S, Quail PH. phyA dominates in transduction of red-light signals to rapidly responding genes at the initiation of Arabidopsis seedling de-etiolation. Plant J 2006, 48:728-742. 10.1111/j.1365-313X.2006.02914.x, 17076805.
85. Lee J, He K, Stolc V, Lee H, Figueroa P, Gao Y, Tongprasit W, Zhao H, Lee I, Deng XW. Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development. The Plant Cell Online 2007, 19:731-749.
86. Larkindale J, Vierling E. Core genome responses involved in acclimation to high temperature. Plant Physiol 2008, 146:748-761. 2245833, 18055584.
87. Li J, Brader G, Palva ET. The WRKY70 Transcription Factor: A Node of Convergence for Jasmonate-Mediated and Salicylate-Mediated Signals in Plant Defense. Plant Cell Online 2004, 16:319-331.
88. Hudson ME, Lisch DR, Quail PH. The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway. Plant J 2003, 34:453-471. 10.1046/j.1365-313X.2003.01741.x, 12753585.
89. Kumagai T, Ito S, Nakamichi N, Niwa Y, Murakami M, Yamashino T, Mizuno T. The common function of a novel subfamily of B-Box zinc finger proteins with reference to circadian-associated events in Arabidopsis thaliana. Biosci Biotechnol Biochem 2008, 72:1539-1549. 10.1271/bbb.80041, 18540109.
90. Tepperman JM, Hudson ME, Khanna R, Zhu T, Chang SH, Wang X, Quail PH. Expression profiling of phyB mutant demonstrates substantial contribution of other phytochromes to red-light-regulated gene expression during seedling de-etiolation. Plant J 2004, 38:725-739. 10.1111/j.1365-313X.2004.02084.x, 15144375.
91. Khanna R, Shen Y, Toledo-Ortiz G, Kikis EA, Johannesson H, Hwang Y-S, Quail PH. Functional profiling reveals that only a small number of phytochrome-regulated early-response genes in arabidopsis are necessary for optimal deetiolation. Plant Cell Online 2006, 18:2157-2171.