MediPlEx - A tool to combine in silico & experimental gene expression profiles of the model legume Medicago truncatula

BMC Research Notes

Volumn 3, Issue , 2010, Pages

  Henckel, Kolja ^a   Küster, Helge ^b   Stutz, Leonhard J ^a   Goesmann, Alexander ^a  

^a BIELEFELD UNIVERSITY   (Germany)

^b LEIBNIZ UNIVERSITY HANNOVER   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77957891922     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-3-262     Document Type: Article

References (47)

1. Medicago truncatula, a model plant for studying the molecular genetics of the Rhizobium-legume symbiosis. D Barker S Bianchi F Blondon Y Dattée G Duc S Essad P Flament P Gallusci G Génier P Guy X Muel J Tourneur J Dénarié T Huguet, Plant Molecular Biology Reporter 1990 8 40 49 10.1007/BF02668879
2. Development of the legume root nodule. NJ Brewin, Annu Rev Cell Biol 1991 7 191 226 10.1146/annurev.cb.07.110191.001203 1809347
3. Molecular and cellular aspects of the arbuscular mycorrhizal symbiosis. MJ Harrison, Annu Rev Plant Physiol Plant Mol Biol 1999 50 361 389 10.1146/annurev.arplant.50.1.361 15012214
4. A new fungal phylum, the Glomeromycota: phylogeny and evolution. A Schüssler D Schwarzott W C, Mycol Res 2001 105 12 1413 1421 10.1017/S0953756201005196
5. Arbuscular mycorrhiza: the mother of plant root endosymbioses. M Parniske, Nat Rev Microbiol 2008 6 10 763 75 10.1038/nrmicro1987 18794914
6. Peace talks and trade deals. Keys to long-term harmony in legume-microbe symbioses. GED Oldroyd MJ Harrison M Udvardi, Plant Physiol 2005 137 4 1205 10 10.1104/pp.104.057661 15824283
7. S Smith D Read, Mycorrhizal Symbiosis Academic Press Second 1997 2
8. Pubmed. http://www.ncbi.nlm.nih.gov/pubmed/
9. The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. J Quackenbush J Cho D Lee F Liang I Holt S Karamycheva B Parvizi G Pertea R Sultana J White, Nucleic Acids Res 2001 29 159 164 10.1093/nar/29.1.159 11125077
10. Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses. H Küster A Becker C Firnhaber N Hohnjec K Manthey A Perlick T Bekel M Dondrup K Henckel A Goesmann F Meyer D Wipf N Requena U Hildebrandt R Hampp U Nehls F Krajinski P Franken A Pühler, Phytochemistry 2007 68 19 32 10.1016/j.phytochem.2006.09.026 17081576
11. Overlaps in the transcriptional profiles of Medicago truncatula roots inoculated with two different Glomus fungi provide insights into the genetic program activated during arbuscular mycorrhiza. N Hohnjec M Vieweg A Pühler A Becker H Küster, Plant Physiol 2005 137 1283 1301 10.1104/pp.104.056572 15778460
12. Identification of gene functions by applying TILLING and insertional mutagenesis strategies on microarray-based expression data. R Thompson P Ratet H Küster, Grain Legumes 2005 41 20 22
13. A gene expression atlas of the model legume Medicago truncatula. VA Benedito I Torres-Jerez JD Murray A Andriankaja S Allen K Kakar M Wandrey J Verdier H Zuber T Ott S Moreau A Niebel T Frickey G Weiller J He X Dai PX Zhao Y Tang MK Udvardi, Plant J 2008 55 3 504 13 10.1111/j.1365-313X.2008.03519.x 18410479
14. Three sequenced legume genomes and many crop species: rich opportunities for translational genomics. SB Cannon GD May SA Jackson, Plant Physiol 2009 151 3 970 7 10.1104/pp.109.144659 19759344
15. Translating Medicago truncatula genomics to crop legumes. ND Young M Udvardi, Curr Opin Plant Biol 2009 12 2 193 201 10.1016/j.pbi.2008.11.005 19162532
16. Dana-Farber Cancer Institute. http://www.dana-farber.org
17. The comparison of gene expression from multiple cDNA libraries. DJ Stekel Y Git F Falciani, Genome Res 2000 10 12 2055 2061 10.1101/gr.GR-1325RR 11116099
18. Exploring root symbiotic programs in the model legume Medicago truncatula using EST analysis. EP Journet D van Tuinen J Gouzy H Crespeau V Carreau MJ Farmer A Niebel T Schiex O Jaillon O Chatagnier L Godiard F Micheli D Kahn V Gianinazzi-Pearson P Gamas, Nucleic Acids Res 2002 30 24 5579 92 10.1093/nar/gkf685 12490726
19. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. R Edgar M Domrachev AE Lash, Nucleic Acids Res 2002 30 207 10 10.1093/nar/30.1.207 11752295
20. NCBI GEO: mining tens of millions of expression profiles-database and tools update. T Barrett DB Troup SE Wilhite P Ledoux D Rudnev C Evangelista IF Kim A Soboleva M Tomashevsky R Edgar, Nucleic Acids Res 2007 35 Database 760 5 10.1093/nar/gkl887 17099226
21. ArrayExpress-a public database of microarray experiments and gene expression profiles. H Parkinson M Kapushesky M Shojatalab N Abeygunawardena R Coulson A Farne E Holloway N Kolesnykov P Lilja M Lukk R Mani T Rayner A Sharma E William U Sarkans A Brazma, Nucleic Acids Res 2007 35 747 50 10.1093/nar/gkl995 (Pubitemid 46056303)
22. The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface. J Chen P Zhao D Massaro L Clerch R Almon D DuBois W Jusko E Hoffman, Nucleic Acids Res 2004 1 32 578 81 10.1093/nar/gkh003
23. The Stanford Microarray Database. G Sherlock T Hernandez-Boussard A Kasarskis G Binkley J Matese S Dwight M Kaloper S Weng H Jin C Ball M Eisen P Spellman P Brown D Botstein J Cherry, Nucleic Acids Res 2001 1, 29 1 152 5 10.1093/nar/29.1.152
24. BarleyBase/PLEXdb. RP Wise RA Caldo L Hong L Shen E Cannon JA Dickerson, Methods Mol Biol 2007 406 347 363 full-text 18287702
25. TRUNCATULIX - a data warehouse for the legume community. K Henckel K Runte T Bekel M Dondrup T Jakobi H Küster A Goesmann, BMC Plant Biol 2009 9 19 10.1186/1471-2229-9-19 19210766
26. Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology. F Cheung B Haas S Goldberg G May Y Xiao C Town, BMC Genomics 2006 7 272 17062153
27. Annotating the genome of Medicago truncatula. C Town, Current Opinion in Plant Biology 2006 9 2 122 127 10.1016/j.pbi.2006.01.004 16458040
28. The Sequence Analysis and Management System - SAMS-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies. T Bekel K Henckel H Küster F Meyer V Mittard Runte H Neuweger D Paarmann O Rupp M Zakrzewski A Pühler J Stoye A Goesmann, J Biotechnol 2009 140 1-2 3 12 10.1016/j.jbiotec.2009.01. 006 19297685
29. Java. http://java.sun.com/
30. Transcriptional snapshots provide insights into the molecular basis of arbuscular mycorrhiza in the model legume Medicago truncatula. N Hohnjec K Henckel T Bekel J Gouzy M Dondrup A Goesmann H Küster, Functional Plant Biology 2006 33 8 737 748 10.1071/FP06079 (Pubitemid 44162018)
31. A Medicago truncatula phosphate transporter indispensable for the arbuscular mycorrhizal symbiosis. H Javot RV Penmetsa N Terzaghi DR Cook MJ Harrison, Proc Natl Acad Sci USA 2007 104 5 1720 5 10.1073/pnas.0608136104 17242358
32. A member of the germin-like protein family is a highly conserved mycorrhiza-specific induced gene. J Doll B Hause K Demchenko K Pawlowski F Krajinski, Plant Cell Physiol 2003 44 11 1208 14 10.1093/pcp/pcg153 14634158
33. Transcriptional changes in response to arbuscular mycorrhiza development in the model plant Medicago truncatula. A Wulf K Manthey J Doll AM Perlick B Linke T Bekel F Meyer P Franken H Küster F Krajinski, Mol Plant Microbe Interact 2003 16 4 306 14 10.1094/MPMI.2003.16.4.306 12744459
34. Combined transcriptome profiling reveals a novel family of arbuscular mycorrhizal-specific Medicago truncatula lectin genes. A Frenzel K Manthey AM Perlick F Meyer A Pühler H Kuster F Krajinski, Mol Plant Microbe Interact 2005 18 8 771 82 10.1094/MPMI-18-0771 16134889
35. Transcript profiling coupled with spatial expression analyses reveals genes involved in distinct developmental stages of an arbuscular mycorrhizal symbiosis. J Liu LA Blaylock G Endre J Cho CD Town KA VandenBosch MJ Harrison, Plant Cell 2003 15 9 2106 23 10.1105/tpc.014183 12953114
36. Identification of mycorrhiza-regulated genes with arbuscule development-related expression profile. U Grunwald O Nyamsuren M Tamasloukht L Lapopin A Becker P Mann V Gianinazzi-Pearson F Krajinski P Franken, Plant Mol Biol 2004 55 4 553 66 10.1007/s11103-004-1303-y 15604700
37. Simcluster: clustering enumeration gene expression data on the simplex space. RZN Vencio L Varuzza CA de B Pereira H Brentani I Shmulevich, BMC Bioinformatics 2007 8 246 10.1186/1471-2105-8-246 17625017
38. Serial analysis of gene expression. VE Velculescu L Zhang B Vogelstein KW Kinzler, Science 1995 270 5235 484 487 10.1126/science.270.5235.484 7570003
39. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. S Brenner M Johnson J Bridgham G Golda DH Lloyd D Johnson S Luo S McCurdy M Foy M Ewan R Roth D George S Eletr G Albrecht E Vermaas SR Williams K Moon T Burcham M Pallas RB DuBridge J Kirchner K Fearon J Mao K Corcoran, Nat Biotechnol 2000 18 6 630 634 10.1038/76469 10835600
40. Large scale cDNA sequencing for analysis of quantitative and qualitative aspects of gene expression. K Okubo N Hori R Matoba T Niiyama A Fukushima Y Kojima K Matsubara, Nat Genet 1992 2 3 173 179 10.1038/ng1192-173 1345164
41. Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. MN Bainbridge RL Warren M Hirst T Romanuik T Zeng A Go A Delaney M Griffith M Hickenbotham V Magrini ER Mardis MD Sadar AS Siddiqui MA Marra SJM Jones, BMC Genomics 2006 7 246 10.1186/1471-2164-7-246 17010196
42. J Aitchison, The Statistical Annalysis of Compositional Data. Monographs on Statistics and Applied Probability London: Chapman and Hall 1986
43. Simplicial inference. Algebraic methods in statistics and probability. AMS special session on algebraic methods in statistics. J Aitchison, American Mathematical Society. Contemp. Math 2001 287 1 22
44. Basic Local Alignment Search Tool. S Altschul W Gish W Miller E Myers D Lipman, J Mol Biol 1990 215 402 410
45. InterPro and InterProScan: tools for protein sequence classification and comparison. N Mulder R Apweiler, Methods Mol Biol 2007 396 59 70 full-text 18025686
46. Profile hidden Markov models. SR Eddy, Bioinformatics 1998 14 9 755 63 10.1093/bioinformatics/14.9.755 9918945
47. R Development Core Team, R: A Language and Environment for Statistical Computing R Foundation for Statistical Computing, Vienna, Austria 2008 http://www.R-project.org [ISBN 3-900051-07-0