Riaño-Pachón DM, Ruzicic S, Dreyer I, Mueller-Roeber B: PlnTFDB: an integrative plant transcription factor database. BMC Bioinformatics. 2007, 8:

Google Scholar

Singh K, Foley RC, Oñate-Sánchez L: Transcription factors in plant defense and stress responses. Curr Opin Plant Biol. 2002, 5 (5): 430-436. 10.1016/S1369-5266(02)00289-3.

Article
CAS
PubMed
Google Scholar

Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L: MYB transcription factors in Arabidopsis. Trends Plant Sci. 2010, 15 (10): 573-581. 10.1016/j.tplants.2010.06.005.

Article
CAS
PubMed
Google Scholar

Carrasco JL, Ancillo G, Mayda E, Vera P: A novel transcription factor involved in plant defense endowed with protein phosphatase activity. EMBO. 2003, 22: 3376-3384. 10.1093/emboj/cdg323.

Article
CAS
Google Scholar

Bulyk ML: Computational prediction of transcription-factor binding site locations. Genome Biol. 2003, 5:

Google Scholar

Cartharius K, Frech K, Grote K, Klocke B, Haltmeier M, Klingenhoff A, Frisch M, Bayerlein M, Werner T: MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics. 2005, 21 (13): 2933-2942. 10.1093/bioinformatics/bti473.

Article
CAS
PubMed
Google Scholar

Pertea M, Mount SM, Salzberg SL: A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana. BMC Bioinformatics. 2007, 8: 159+-10.1186/1471-2105-8-159.

Article
PubMed Central
PubMed
Google Scholar

Fauteux F, Stromvik M: Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae. BMC Plant Biol. 2009, 9: 126+-10.1186/1471-2229-9-126.

Article
PubMed Central
PubMed
Google Scholar

Vandepoele K, Casneuf T, Van de Peer Y: Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics. Genome Biol. 2007, 7 (11):

Leelavati N, Ovcharenko I: Identifying regulatory elements in eukaryotic genomes. Brief Funct Genomic Proteomic. 2009, 8 (4): 215-230. 10.1093/bfgp/elp014.

Article
Google Scholar

Chekmenev DS, Haid C, Kel AE: P-Match: transcription factor binding site search by combining patterns and weight matrices. Nucleic Acids Res. 2005, 33: W432-W437. 10.1093/nar/gki441.

Article
PubMed Central
CAS
PubMed
Google Scholar

Loots GG, Ovcharenko I, Pachter L, Dubchak I, Rubin EM: rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res. 2002, 12 (5): 832-839.

Article
PubMed Central
PubMed
Google Scholar

Kel AE, Voss N, Jauregui R, Kel-Margoulis OV, Wingender E: Beyond microarrays: Finding key transcription factors controlling signal transduction pathways. BMC Bioinformatics. 2006, 7 (S-2):

Bülow L, Engelmann S, Schindler M, Hehl R: AthaMap, integrating transcriptional and post-transcriptional data. Nucleic Acids Res. 2009, 37 (Database-Issue): D983-D986.

Article
PubMed Central
PubMed
Google Scholar

Palaniswamy SK, James S, Sun H, Lamb RS, Davuluri RV, Grotewold E: AGRIS and AtRegNet: A platform to link cis-regulatory elements and transcription factors into regulatory networks. Plant Physiol. 2006, 140 (3): 818-829. 10.1104/pp.105.072280.

Article
PubMed Central
CAS
PubMed
Google Scholar

Rombauts S, Florquin K, Lescot M, Rouzé P, van de Peer, c: Computational approaches to identify promoters and cis-regulatory elements in plant genomes. Plant Physiol. 2003, 132 (3): 1162-1176. 10.1104/pp.102.017715.

Article
PubMed Central
CAS
PubMed
Google Scholar

Wingender E, Chen X, Fricke E, Geffers R, Hehl R, Liebich I, Krull M, Matys V, Michael H, Ohnhauser R, Pruss M, Schacherer F, Thiele S, Urbach S: The TRANSFAC system on gene expression regulation. Nucleic Acids Res. 2001, 29: 281-283. 10.1093/nar/29.1.281.

Article
PubMed Central
CAS
PubMed
Google Scholar

Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B: JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 2007, 32: D91-D94.

Article
Google Scholar

Gabdoulline RR, Eckweiler D, Kel AE, Stegmaier P: 3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations. Nucleic Acids Res. 2012, 40 (Web-Server-Issue): 180-185.

Article
Google Scholar

Horspool NR: Practical fast searching in strings. Softw Pract Exp. 1980, 10 (6): 501-506. 10.1002/spe.4380100608.

Article
Google Scholar

Ulmasov T, Hagen G, Guilfoyle TJ: ARF1, a transcription factor that binds to auxin response elements. Science. 1997, 276: 1865-1868. 10.1126/science.276.5320.1865.

Article
CAS
PubMed
Google Scholar

Ramakrishnan S, Rakesh A: Mining sequential patterns: generalizations and performance improvements. Proceedings 5th International Conference Extending Database Technology, EDBT. Avignon, France. 1996, London: Springer-Verlag, 3-17.

Google Scholar

Tan PN, Kumar V, Srivastava J: Selecting the right interestingness measure for association patterns. Proceedings of the Eighth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, KDD ’02. 2002, Edmonton, AB, Canada, 32-41.

Chapter
Google Scholar

Geng L, Hamilton HJ: Interestingness measures for data mining: a survey. ACM Comput Surv. 2006, 38 (3):

Steinbach M, Tan PN, Xiong H, Kumar V: Objective measures for association pattern analysis. Contemp Math. 2007, 443: 205-226.

Article
Google Scholar

Agrawal R, Imielinski T, Swami A: Mining association rules between sets of items in large databases. ACM SIGMOD Intl. Conf. Management of Data. Washington, D.C. 1993, New York: ACM, 207-216.

Google Scholar

Merceron A, Yacef K: Interestingness measures for association rules in educational data. Proceedings of Educational Data Mining 2008: 1st International Conference on Educational Data Mining. 2008, Montreal, Quebec, 57-66.

Google Scholar

Jaccard P: Ètude comparative de la distribution florale dans une portion des Alpes et des Jura. Bull Société Vaudoise des Sci Naturelles. 1901, 37: 547-579.

Google Scholar

Cohen J: A coefficient of agreement for nominal scales. Educ Psychol Meas. 1960, 20: 37-46. 10.1177/001316446002000104.

Article
Google Scholar

Good IJ: booktitle=The Estimation of Probabilities: An Essay on Modern Bayesian Methods, Volume 30 of Research Monograph,. 1965, Cambridge: M.I.T. Press

Google Scholar

Brin S, Motwani R, Ullman JD, Tsur S: Dynamic itemset counting and implication rules for market basket data. SIGMOD 1997, Proceedings ACM SIGMOD International Conference on Management of Data. Tucson, Arizona. 1997, New York: ACM, 255-264.

Chapter
Google Scholar

Cramér H: Mathematical Methods of Statistics. Princeton mathematical series. 1946, Princeton University Press

Google Scholar

Deming WE, Stephan FF: On a least squares adjustment of a sampled frequency table when the expected marginal totals are known. Ann Math Stat. 1940, 11 (4): 427-444. 10.1214/aoms/1177731829.

Article
Google Scholar

Mosteller F: Association and estimation in contingency tables. J Am Stat Assoc. 1968, 63 (321): 1-28. 10.2307/2283825.

Google Scholar

Tan PN, Kumar V, Srivastava J: Selecting the right objective measure for association analysis. Inf Syst. 2004, 29: 293-313. 10.1016/S0306-4379(03)00072-3.

Article
Google Scholar

Tremblay A, Hosseini P, Alkharouf NW, Li S, Matthews BF: Gene expression in leaves of susceptible Glycine max during infection with Phakopsora pachyrhizi using next generation sequencing. Sequencing. 2011, 14-

Google Scholar

Peterson JD, Umayam LA, Dickinson TM, Hickey EK, White O: The comprehensive microbial resource. Nucleic Acids Res. 2001, 29: 123-125. 10.1093/nar/29.1.123.

Article
PubMed Central
CAS
PubMed
Google Scholar

Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25 (14): 1754-1760. 10.1093/bioinformatics/btp324.

Article
PubMed Central
CAS
PubMed
Google Scholar

Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008, 5 (7): 621-628. 10.1038/nmeth.1226.

Article
CAS
PubMed
Google Scholar

Rushton PJ, Somssich IE, Ringler P, Shen QJ: WRKY transcription factors. Trends Plant Sci. 2010, 15 (5): 247-258. 10.1016/j.tplants.2010.02.006.

Article
CAS
PubMed
Google Scholar

Eulgem T: Dissecting the WRKY web of plant defense regulators. PLoS Pathogy. 2006, 2 (11):

Eulgem T, Rushton PJ, Robatzek S, Somssich IE: The WRKY superfamily of plant transcription factors. Journal. 2000, 5 (5): 199-206.

CAS
Google Scholar

Eulgem T, Somssich IE: Networks of WRKY transcription factors in defense signaling. Curr Opin Plant Biol. 2007, 10 (4): 366-371. 10.1016/j.pbi.2007.04.020.

Article
CAS
PubMed
Google Scholar

Pandey SP, Somssich IE: The role of WRKY transcription factors in plant immunity. Plant Physiol. 2009, 150 (4): 1648-1655. 10.1104/pp.109.138990.

Article
PubMed Central
CAS
PubMed
Google Scholar

Yu D, Chen C, Chen Z: Evidence for an important role of WRKY DNA binding proteins in the regulation of NPR1 gene expression. Plant Cell. 2001, 13 (7): 1527-1540.

Article
PubMed Central
CAS
PubMed
Google Scholar

Dong X: NPR1, all things considered. Curr Opin Plant Biol. 2004, 7 (5): 547-552. 10.1016/j.pbi.2004.07.005.

Article
CAS
PubMed
Google Scholar

Sibout R, Sukumar P, Hettiarachchi C, Holm M, Muday GK, Hardtke CS: Opposite root growth phenotypes of hy5 versus hy5 hyh mutants correlate with increased constitutive auxin signaling. PLoS Genet. 2004, 2 (11):

Cluis CP, Mouchel CF, Hardtke CS: The Arabidopsis transcription factor HY5 integrates light and hormone signaling pathways. Plant. 2004, 38 (2): 332-347. 10.1111/j.1365-313X.2004.02052.x.

Article
CAS
Google Scholar

Prasad BRVP, Kumar SV, Nandi A, Chattopadhyay S: Functional interconnections of HY1 with MYC2 and HY5 in Arabidopsis seedling development. BMC Plant Biol. 2012, 12 (37):

Boter M, Ruíz-Rivero O, Abdeen A, Prat S: Conserved MYC transcription factors play a key role in jasmonate signaling both in tomato and Arabidopsis. Journal. 2004, 18 (13): 1577-1591.

CAS
Google Scholar

Abe H, Urao T, Itom T, Seki M, Shinozaki K, Yamaguchi-Shinozaki K: Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling. Plant Cell. 2003, 15: 63-78. 10.1105/tpc.006130.

Article
PubMed Central
CAS
PubMed
Google Scholar

Kaplan-Levy RN, Brewer PB, Quon T, Smyth DR: The trihelix family of transcription factors - light, stress and development. Trends Plant Sci. 2012, 17 (3): 163-171. 10.1016/j.tplants.2011.12.002.

Article
CAS
PubMed
Google Scholar

Xie ZM, Zou HF, Lei G, Wei W, Zhou QY, Niu CF, Liao Y, Tian AG, Ma B, Zhang WK, Zhang JS, Chen SY: Soybean trihelix transcription factors GmGT-2A and GmGT-2B improve plant tolerance to abiotic stresses in transgenic Arabidopsis. PLoS ONE. 2009, 4 (9): e6898-10.1371/journal.pone.0006898.

Article
PubMed Central
PubMed
Google Scholar

Pison G, Struyf A, Rousseeuw PJ: Displaying a clustering with CLUSPLOT. Comput Stat Data Anal. 1999, 30 (4): 381-392. 10.1016/S0167-9473(98)00102-9.

Article
Google Scholar

Keilwagen J, Grau J, Paponov IA, Posch S, Strickert M, Grosse I: De-novo discovery of differentially abundant transcription factor binding sites including their positional preference. PLoS Comput Biology. 2011, 7 (2): e1001070+-

Article
CAS
Google Scholar

Yamamoto YY, Obokata J: ppdb: a plant promoter database. Nucleic Acids Res. 2008, 36 (Database issue): D977-D981.

PubMed Central
CAS
PubMed
Google Scholar

Chang WCC, Lee TYY, Huang HDD, Huang HYY, Pan RLL: PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups. BMC Genomics. 2008, 9: 561+-10.1186/1471-2164-9-561.

Article
PubMed Central
PubMed
Google Scholar