AthaMap web tools for the analysis of transcriptional and posttranscriptional regulation of gene expression in arabidopsis thaliana

Methods in Molecular Biology

Volumn 1158, Issue , 2014, Pages 139-156

  Hehl, Reinhard ^a   Bülow, Lorenz ^a  

^a NONE

Author keywords

Bioinformatics; Databases; Diurnal regulation; Gene expression; Posttranscriptional regulation; Transcriptional regulation; Web server

Indexed keywords

TRANSCRIPTION FACTOR; PLANT RNA;

ARABIDOPSIS THALIANA; ARTICLE; BINDING SITE; BIOINFORMATICS; DATA BASE; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; NONHUMAN; ONLINE SYSTEM; PLANT GENOME; PRIORITY JOURNAL; PROTEIN RNA BINDING; TRANSCRIPTION REGULATION; WEB BROWSER; ARABIDOPSIS; BIOLOGY; COMPUTER PROGRAM; GENETIC DATABASE; GENETIC TRANSCRIPTION; GENETICS; PROCEDURES; RNA PROCESSING;

ARABIDOPSIS THALIANA;

ARABIDOPSIS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION REGULATION, PLANT; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, PLANT; SOFTWARE; TRANSCRIPTION, GENETIC; WEB BROWSER;

EID: 84907908639     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-0700-7_9     Document Type: Article

References (71)

1. Steffens NO, Galuschka C, Schindler M, Bülow L, Hehl R (2004) AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome. Nucleic Acids Res 32(1):D368-D372
2. Hertz GZ, Stormo GD (1999) Identifying DNA and protein patterns with statistically signifi cant alignments of multiple sequences. Bioinformatics 15(7-8):563-577
3. Steffens NO, Galuschka C, Schindler M, Bülow L, Hehl R (2005) AthaMap web tools for database- assisted identifi cation of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana . Nucleic Acids Res 33:W397-W402
4. Bülow L, Steffens NO, Galuschka C, Schindler M, Hehl R (2006) AthaMap: from in silico data to real transcription factor binding sites. Silico Biol 6(3):243-252
5. Bülow L, Engelmann S, Schindler M, Hehl R (2009) AthaMap, integrating transcriptional and post-transcriptional data. Nucleic Acids Res 37(Database issue):D983-D986
6. Bülow L, Bolívar JC, Ruhe J, Brill Y, Hehl R (2012) ‘MicroRNA Targets’, A new AthaMap web-tool for genome-wide identifi cation of miRNA targets in Arabidopsis thaliana . BioData Min 5:7
7. Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ (2005) Elucidation of the small RNA component of the transcriptome. Science 309(5740):1567-1569
8. Axtell MJ, Jan C, Rajagopalan R, Bartel DP (2006) A two-hit trigger for siRNA biogenesis in plants. Cell 127(3):565-577
9. Rajagopalan R, Vaucheret H, Trejo J, Bartel DP (2006) A diverse and evolutionarily fl uid set of microRNAs in Arabidopsis thaliana. Genes Dev 20(24):3407-3425
10. Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Carrington JC (2007) Genome-wide profi ling and analysis of Arabidopsis siRNAs. PLoS Biol 5(3):e57
11. Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC (2007) High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One 2(2):e219
12. Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, Givan SA, Kasschau KD, Carrington JC (2007) Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNAand tasiRNA-directed targeting. Plant Cell 19(3):926-942
13. Kozomara A, Griffi ths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39(Database issue):D152-D157
14. Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39(Suppl 2):W155-W159
15. Quadrana L, Almeida J, Otaiza SN, Duffy T, Correa da Silva JV, de Godoy F, Asis R, Bermudez L, Fernie AR, Carrari F, Rossi M (2013) Transcriptional regulation of tocopherol biosynthesis in tomato. Plant Mol Biol 81(3):309-325
16. Donner TJ, Scarpella E (2013) Transcriptional control of early vein expression of CYCA2; 1 and CYCA2;4 in Arabidopsis leaves. Mech Dev 130(1):14-24
17. Barah P, Winge P, Kusnierczyk A, Tran DH, Bones AM (2013) Molecular signatures in Arabidopsis thaliana in response to insect attack and bacterial infection. PLoS One 8(3):e58987
18. Michael TP, Mockler TC, Breton G, McEntee C, Byer A, Trout JD, Hazen SP, Shen R, Priest HD, Sullivan CM, Givan SA, Yanovsky M, Hong F, Kay SA, Chory J (2008) Network discovery pipeline elucidates conserved time-of- dayspecifi c cis-regulatory modules. PLoS Genet 4(2):e14
19. Priest HD, Filichkin SA, Mockler TC (2009) Cis-Regulatory elements in plant cell signaling. Curr Opin Plant Biol 12(5):643-649
20. Marin-De La, Rosa N, Alabadi D, Blazquez MA, Arana MV (2011) Integrating circadian and gibberellin signaling in Arabidopsis: possible links between the circadian clock and the AtGID1 transcription. Plant Signal Behav 6(9): 1411-1413
21. Nagel DH, Kay SA (2012) Complexity in the wiring and regulation of plant circadian networks. Curr Biol 22(16):R648-R657
22. Hazen SP, Schultz TF, Pruneda-Paz JL, Borevitz JO, Ecker JR, Kay SA (2005) LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms. Proc Natl Acad Sci U S A 102(29):10387-10392
23. Giraud E, Ng S, Carrie C, Duncan O, Low J, Lee CP, Van Aken O, Millar AH, Murcha M, Whelan J (2010) TCP transcription factors link the regulation of genes encoding mitochondrial proteins with the circadian clock in Arabidopsis thaliana. Plant Cell 22(12):3921-3934
24. Kosugi S, Ohashi Y (2002) DNA binding and dimerization specifi city and potential targets for the TCP protein family. Plant J 30(3): 337-348
25. Viola IL, Reinheimer R, Ripoll R, Manassero NG, Gonzalez DH (2012) Determinants of the DNA binding specifi city of class I and class II TCP transcription factors. J Biol Chem 287(1): 347-356
26. Galuschka C, Schindler M, Bülow L, Hehl R (2007) AthaMap web-tools for the analysis and identifi cation of co-regulated genes. Nucleic Acids Res 35:D857-D862
27. Bülow L, Brill Y, Hehl R (2010) AthaMapassisted transcription factor target gene identifi cation in Arabidopsis thaliana. Database (Oxford) 2010:baq034
28. Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, Radenbaugh A, Singh S, Swing V, Tissier C, Zhang P, Huala E (2008) The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res 36(Database issue):D1009-D1014
29. Mewes HW, Ruepp A, Theis F, Rattei T, Walter M, Frishman D, Suhre K, Spannagl M, Mayer KF, Stumpflen V, Antonov A (2010) MIPS: curated databases and comprehensive secondary data resources in 2010. Nucleic Acids Res 39(Database issue):D220-D224
30. Shahmuradov IA, Gammerman AJ, Hancock JM, Bramley PM, Solovyev VV (2003) PlantProm: a database of plant promoter sequences. Nucleic Acids Res 31(1):114-117
31. Hehl R, Bülow L (2008) Internet resources for gene expression analysis in Arabidopsis thaliana. Curr Genomics 9:375-380
32. Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, Tanimoto M, Chow A, Steinhauser D, Persson S, Provart NJ (2009) Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant Cell Environ 32(12):1633-1651
33. Brady SM, Provart NJ (2009) Web-queryable large-scale data sets for hypothesis generation in plant biology. Plant Cell 21(4):1034-1051
34. Mejia-Guerra MK, Pomeranz M, Morohashi K, Grotewold E (2012) From plant gene regulatory grids to network dynamics. Biochim Biophys Acta 1819(5):454-465
35. Davuluri RV, Sun H, Palaniswamy SK, Matthews N, Molina C, Kurtz M, Grotewold E (2003) AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinforma 4(1):25
36. O’Connor TR, Dyreson C, Wyrick JJ (2005) Athena: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences. Bioinformatics 21(24):4411-4413
37. Obayashi T, Kinoshita K, Nakai K, Shibaoka M, Hayashi S, Saeki M, Shibata D, Saito K, Ohta H (2007) ATTED-II: a database of coexpressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res 35(Database issue): D863-D869
38. Chen Y-A, Wen Y-C, Chang W-C (2012) AtPAN: an integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana. BMC Genomics 13:85
39. Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27(1):297-300
40. Rombauts S, Dehais P, Van Montagu M, Rouze P (1999) PlantCARE, a plant cis-acting regulatory element database. Nucleic Acids Res 27(1): 295-296
41. Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Münch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, Wingender E (2003) TRANSFAC: transcriptional regulation, from patterns to profi les. Nucleic Acids Res 31(1):374-378
42. Ding J, Hu H, Li X (2012) Thousands of cisregulatory sequence combinations are shared by Arabidopsis and poplar. Plant Physiol 158(1):145-155
43. Perez-Rodriguez P, Riano-Pachon DM, Correa LG, Rensing SA, Kersten B, Mueller-Roeber B (2010) PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res 38(Database issue): D822-D827
44. Bailey TL (2008) Discovering sequence motifs. Methods Mol Biol 452:231-251
45. Koschmann J, Machens F, Becker M, Niemeyer J, Schulze J, Bülow L, Stahl DJ, Hehl R (2012) Integration of bioinformatics and synthetic promoters leads to the discovery of novel elicitor- responsive cis-regulatory sequences in Arabidopsis. Plant Physiol 160:178-191
46. van Helden J (2003) Regulatory sequence analysis tools. Nucleic Acids Res 31(13): 3593-3596
47. Thomas-Chollier M, Defrance M, Medina-Rivera A, Sand O, Herrmann C, Thieffry D, van Helden J (2011) RSAT 2011: regulatory sequence analysis tools. Nucleic Acids Res 39(Web Server issue):W86-W91
48. Toufi ghi K, Brady SM, Austin R, Ly E, Provart NJ (2005) The Botany Array Resource: e-northerns, expression angling, and promoter analyses. Plant J 43(1):153-163
49. Bailey TL, Elkan C (1995) The value of prior knowledge in discovering motifs with MEME. Proc Int Conf Intell Syst Mol Biol 3:21-29
50. Roth FP, Hughes JD, Estep PW, Church GM (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol 16(10):939-945
51. GuhaThakurta D, Stormo GD (2001) Identifying target sites for cooperatively binding factors. Bioinformatics 17(7):608-621
52. Liu X, Brutlag DL, Liu JS (2001) BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co- expressed genes. Pac Symp Biocomput, pp 127-138
53. Eskin E, Pevzner PA (2002) Finding composite regulatory patterns in DNA sequences. Bioinformatics 18(Suppl 1):S354-S363
54. Jensen ST, Liu JS (2004) BioOptimizer: a Bayesian scoring function approach to motif discovery. Bioinformatics 20(10):1557-1564
55. Che D, Jensen S, Cai L, Liu JS (2005) BEST: binding-site estimation suite of tools. Bioinformatics 21(12):2909-2911
56. Mahony S, Benos PV (2007) STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res 35(Web Server issue): W253-W258
57. Yan T, Yoo D, Berardini TZ, Mueller LA, Weems DC, Weng S, Cherry JM, Rhee SY (2005) PatMatch: a program for fi nding patterns in peptide and nucleotide sequences. Nucleic Acids Res 33(Web Server issue): W262-W266
58. Xie F, Zhang B (2010) Target-align: a tool for plant microRNA target identifi cation. Bioinformatics 26(23):3002-3003
59. Backman TW, Sullivan CM, Cumbie JS, Miller ZA, Chapman EJ, Fahlgren N, Givan SA, Carrington JC, Kasschau KD (2008) Update of ASRP: the Arabidopsis small RNA project database. Nucleic Acids Res 36(Database issue): D982-D985
60. Meyers BC, Vu TH, Tej SS, Ghazal H, Matvienko M, Agrawal V, Ning J, Haudenschild CD (2004) Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing. Nat Biotechnol 22(8):1006-1011
61. Winter D, Vinegar B, Nahal H, Ammar R, Wilson GV, Provart NJ (2007) An “electronic fl uorescent pictograph” browser for exploring and analyzing large-scale biological data sets. PLoS One 2(1):e718
62. Dupl’akova N, Renak D, Hovanec P, Honysova B, Twell D, Honys D (2007) Arabidopsis Gene Family Profi ler (aGFP)-user-oriented transcriptomic database with easy-to-use graphic interface. BMC Plant Biol 7(39):39
63. Baginsky S, Gruissem W (2006) Arabidopsis thaliana proteomics: from proteome to genome. J Exp Bot 57(7):1485-1491
64. Kawaguchi R, Bailey-Serres J (2005) mRNA sequence features that contribute to translational regulation in Arabidopsis. Nucleic Acids Res 33(3):955-965
65. Dolan L (2001) Root patterning: SHORT ROOT on the move. Curr Biol 11(23): R983-R985
66. Heazlewood JL, Verboom RE, Tonti-Filippini J, Small I, Millar AH (2007) SUBA: the Arabidopsis subcellular database. Nucleic Acids Res 35(Database issue):D213-D218
67. Schwacke R, Schneider A, van der Graaff E, Fischer K, Catoni E, Desimone M, Frommer WB, Flugge UI, Kunze R (2003) ARAMEMNON, a novel database for Arabidopsis integral membrane proteins. Plant Physiol 131(1):16-26
68. Baerenfaller K, Grossmann J, Grobei MA, Hull R, Hirsch-Hoffmann M, Yalovsky S, Zimmermann P, Grossniklaus U, Gruissem W, Baginsky S (2008) Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science 320(5878): 938-941
69. Mockler TC, Michael TP, Priest HD, Shen R, Sullivan CM, Givan SA, McEntee C, Kay SA, Chory J (2007) The DIURNAL project: DIURNAL and circadian expression profi ling, model-based pattern matching, and promoter analysis. Cold Spring Harbor Symp Quantitat Biol 72:353-363
70. Staiger D, Shin J, Johansson M, Davis SJ (2013) The circadian clock goes genomic. Genome Biol 14(6):208
71. The International Arabidopsis Informatics Consortium (2012) Taking the next step: building an Arabidopsis information portal. Plant Cell 24(6):2248-2256