CORNET: A user-friendly tool for data mining and integration

Plant Physiology

Volumn 152, Issue 3, 2010, Pages 1167-1179

  de Bodt, Stefanie ^a   Carvajal, Diana ^a   Hollunder, Jens ^a   van den Cruyce, Joost ^a   Movahedi, Sara ^a   Inzé, Dirk ^a  

^a GHENT UNIVERSITY   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 77949532033     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.109.147215     Document Type: Article

References (77)

1. Achard P, Cheng H, De Grauwe L, Decat J, Schoutteten H, Moritz T, Van Der Straeten D, Peng J, Harberd NP (2006) Integration of plant responses to environmentally activated phytohormonal signals. Science 311: 91-94
2. Achard P, Genschik P (2009) Releasing the brakes of plant growth: how GAs shutdown DELLA proteins. J Exp Bot 60: 1085-1092
3. Achard P, Liao L, Jiang C, Desnos T, Bartlett J, Fu X, Harberd NP (2007) DELLAs contribute to plant photomorphogenesis. Plant Physiol 143: 1163-1172
4. Akiyama K, Chikayama E, Yuasa H, Shimada Y, Tohge T, Shinozaki K, Hirai MY, Sakurai T, Kikuchi J, Saito K (2008) PRIMe: a Web site that assembles tools for metabolomics and transcriptomics. In Silico Biol 8: 339-345
5. Ariizumi T, Murase K, Sun TP, Steber CM (2008) Proteolysis-independent downregulation of DELLA repression in Arabidopsis by the gibberellin receptor GIBBERELLIN INSENSITIVE DWARF1. Plant Cell 20: 2447-2459
6. Avraham S, Tung CW, Ilic K, Jaiswal P, Kellogg EA, McCouch S, Pujar A, Reiser L, Rhee SY, Sachs MM, et al (2008) The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Res 36: D449-D454
7. Bader GD, Betel D, Hogue CWV (2003) BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res 31: 248-250
8. Bannai H, Tamada Y, Maruyama O, Nakai K, Miyano S (2002) Extensive feature detection of N-terminal protein sorting signals. Bioinformatics 18: 298-305
9. Barrett T, Edgar R (2006) Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Methods Enzymol 411: 352-369
10. Brady SM, Provart NJ (2009) Web-queryable large-scale data sets for hypothesis generation in plant biology. Plant Cell 21: 1034-1051
11. Brazma A (2009) Minimum Information About a Microarray Experiment (MIAME): successes, failures, challenges. ScientificWorldJournal 9: 420-423
12. Brown DM, Zeef LAH, Ellis J, Goodacre R, Turner SR (2005) Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. Plant Cell 17: 2281-2295
13. Bruskiewich R, Coe EH, Jaiswal P, McCouch S, Polacco M, Stein L, Vincent L, Ware D (2002) The plant ontology consortium and plant ontologies. Comp Funct Genomics 3: 137-142
14. Cao D, Cheng H, Wu W, Soo HM, Peng J (2006) Gibberellin mobilizes distinct DELLA-dependent transcriptomes to regulate seed germination and floral development in Arabidopsis. Plant Physiol 142: 509-525
15. Casneuf T, Van de Peer Y, Huber W (2007) In situ analysis of cross- hybridisation on microarrays and the inference of expression correlation. BMC Bioinformatics 8: 461
16. Chatr-aryamontri A, Ceol A, Montecchi Palazzi L, Nardelli G, Schneider MV, Castagnoli L, Cesareni G (2007) MINT: the Molecular INTeraction database. Nucleic Acids Res 35: D572-D574
17. Chen H, Huang N, Sun Z (2006) SubLoc: a server/client suite for protein subcellular location based on SOAP. Bioinformatics 22: 376-377
18. Cheng H, Qin L, Lee S, Fu X, Richards DE, Cao D, Luo D, Harberd NP, Peng J (2004) Gibberellin regulates Arabidopsis floral development via suppression of DELLA protein function. Development 131: 1055-1064
19. Claros MG (1995) MitoProt, a Macintosh application for studying mitochondrial proteins. Comput Appl Biosci 11: 441-447
20. Cui J, Li P, Li G, Xu F, Zhao C, Li Y, Yang Z, Wang G, Yu Q, Li Y, et al (2008) AtPID: Arabidopsis thaliana protein interactome database. An integrative platform for plant systems biology. Nucleic Acids Res 36: D999-D1008
21. De Bodt S, Proost S, Vandepoele K, Rouze P, Van de Peer Y (2009) Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression. BMC Genomics 10: 288
22. de Lucas M, Davie ́re JM, Rodriguez-Falco ́n M, Pontin M, Iglesias-Pedraz JM, Lorrain S, Fankhauser C, Bla ́zquez MA, Titarenko E, Prat S (2008) A molecular framework for light and gibberellin control of cell elongation. Nature 451: 480-484
23. de Nooy W, Mrvar A, Batagelj V (2005) Exploratory Social Network Analysis with Pajek. Cambridge University Press, Cambridge, UK
24. Dill A, Sun TP (2001) Synergistic derepression of gibberellin signaling by removing RGA and GAI function in Arabidopsis thaliana. Genetics 159: 777-785
25. Dill A, Thomas SG, Hu J, Steber CM, Sun TP (2004) The Arabidopsis F-box protein SLEEPY1 targets gibberellin signaling repressors for gibberellininduced degradation. Plant Cell 16: 1392-1405
26. Emanuelsson O, Brunak S, von Heijne G, Nielsen H (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2: 953-971
27. Emanuelsson O, Elofsson A, von Heijne G, Cristobal S (2003) In silico prediction of the peroxisomal proteome in fungi, plants and animals. J Mol Biol 330: 443-456
28. Feng S, Martinez C, Gusmaroli G, Wang Y, Zhou J, Wang F, Chen L, Yu L, Iglesias-Pedraz JM, Kircher S, et al (2008) Coordinated regulation of Arabidopsis thaliana development by light and gibberellins. Nature 451: 475-479
29. Fu X, Richards DE, Fleck B, Xie D, Burton N, Harberd NP (2004) The Arabidopsis mutant sleepy1gar2-1 protein promotes plant growth by increasing the affinity of the SCFSLY1 E3 ubiquitin ligase for DELLA protein substrates. Plant Cell 16: 1406-1418
30. Gachon CMM, Langlois-Meurinne M, Henry Y, Saindrenan P (2005) Transcriptional co-regulation of secondary metabolism enzymes in Arabidopsis: functional and evolutionary implications. Plant Mol Biol 58: 229-245
31. Gautier L, Cope L, Bolstad BM, Irizarry RA (2004) Affy: analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20: 307-315
32. Geisler-Lee J, O'Toole N, Ammar R, Provart NJ, Millar AH, Geisler M (2007) A predicted interactome for Arabidopsis. Plant Physiol 145: 317-329
33. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80
34. Goda H, Sasaki E, Akiyama K, Maruyama-Nakashita A, Nakabayashi K, Li W, Ogawa M, Yamauchi Y, Preston J, Aoki K, et al (2008) The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access. Plant J 55: 526-542
35. Goldovsky L, Cases I, Enright AJ, Ouzounis CA (2005) BioLayout(Java): versatile network visualisation of structural and functional relationships. Appl Bioinformatics 4: 71-74
36. Griffiths J, Murase K, Rieu I, Zentella R, Zhang ZL, Powers SJ, Gong F, Phillips AL, Hedden P, Sun TP, et al (2006) Genetic characterization and functional analysis of the GID1 gibberellin receptors in Arabidopsis. Plant Cell 18: 3399-3414
37. Guda C, Fahy E, Subramaniam S (2004) MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins. Bioinformatics 20: 1785-1794
38. Gutierrez RA, Lejay LV, Dean A, Chiaromonte F, Shasha DE, Coruzzi GM (2007) Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biol 8: R7
39. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, et al (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32: D258-D261
40. Heazlewood JL, Verboom RE, Tonti-Filippini J, Small I, Millar AH (2007) SUBA: the Arabidopsis Subcellular Database. Nucleic Acids Res 35: D213-D218
41. Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A, et al (2004) IntAct: an open source molecular interaction database. Nucleic Acids Res 32: D452-D455
42. Høglund A, Donnes P, Blum T, Adolph HW, Kohlbacher O (2006) MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition. Bioinformatics 22: 1158-1165
43. Horan K, Jang C, Bailey-Serres J, Mittler R, Shelton C, Harper JF, Zhu JK, Cushman JC, Gollery M, Girke T (2008) Annotating genes of known and unknown function by large-scale coexpression analysis. Plant Physiol 147: 41-57
44. Horton P, Park KJ, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res 35: W585-W587
45. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, et al (2009) InterPro: the integrative protein signature database. Nucleic Acids Res 37: D211-D215
46. Ilic K, Kellogg EA, Jaiswal P, Zapata F, Stevens PF, Vincent LP, Avraham S, Reiser L, Pujar A, Sachs MM, et al (2007) The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiol 143: 587-599
47. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP (2003a) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31: e15
48. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP (2003b) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264
49. Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, D'Angelo C, Bornberg-Bauer E, Kudla J, Harter K (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J 50: 347-363
50. King KE, Moritz T, Harberd NP (2001) Gibberellins are not required for normal stem growth in Arabidopsis thaliana in the absence of GAI and RGA. Genetics 159: 767-776
51. Lee S, Cheng H, King KE, Wang W, He Y, Hussain A, Lo J, Harberd NP, Peng J (2002) Gibberellin regulates Arabidopsis seed germination via RGL2, a GAI/RGA-like gene whose expression is up-regulated following imbibition. Genes Dev 16: 646-658
52. Lisso J, Steinhauser D, Altmann T, Kopka J, Mussig C (2005) Identification of brassinosteroid-related genes by means of transcript co-response analyses. Nucleic Acids Res 33: 2685-2696
53. Manfield IW, Jen CH, Pinney JW, Michalopoulos I, Bradford JR, Gilmartin PM, Westhead DR (2006) Arabidopsis Co-expression Tool (ACT): Web server tools for microarray-based gene expression analysis. Nucleic Acids Res 34: W504-W509
54. Mutwil M, Øbro J, Willats WGT, Persson S (2008) GeneCAT: novel Webtools that combine BLAST and co-expression analyses. Nucleic Acids Res 36: W320-W326
55. Nair R, Rost B (2005) Mimicking cellular sorting improves prediction of subcellular localization. J Mol Biol 348: 85-100
56. Nakajima M, Shimada A, Takashi Y, Kim YC, Park SH, Ueguchi-Tanaka M, Suzuki H, Katoh E, Iuchi S, Kobayashi M, et al (2006) Identification and characterization of Arabidopsis gibberellin receptors. Plant J 46: 880-889
57. Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K (2009) ATTED-II provides coexpressed gene networks for Arabidopsis. Nucleic Acids Res 37: D987-D991
58. Obayashi T, Kinoshita K, Nakai K, Shibaoka M, Hayashi S, Saeki M, Shibata D, Saito K, Ohta H (2007) ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res 35: D863-D869
59. Pujar A, Jaiswal P, Kellogg EA, Ilic K, Vincent L, Avraham S, Stevens P, Zapata F, Reiser L, Rhee SY, et al (2006) Whole-plant growth stage ontology for angiosperms and its application in plant biology. Plant Physiol 142: 414-428
60. Rautengarten C, Steinhauser D, Bussis D, Stintzi A, Schaller A, Kopka J, Altmann T (2005) Inferring hypotheses on functional relationships of genes: analysis of the Arabidopsis thaliana subtilase gene family. PLoS Comput Biol 1: e40
61. Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia- Hernandez M, Huala E, Lander G, Montoya M, et al (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res 31: 224-228
62. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D (2004) The Database of Interacting Proteins: 2004 update. Nucleic Acids Res 32: D449-D451
63. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU (2005) A gene expression map of Arabidopsis thaliana development. Nat Genet 37: 501-506
64. Schwechheimer C (2008) Understanding gibberellic acid signaling: are we there yet? Curr Opin Plant Biol 11: 9-15
65. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504
66. Small I, Peeters N, Legeai F, Lurin C (2004) Predotar: a tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics 4: 1581-1590
67. Srinivasasainagendra V, Page GP, Mehta T, Coulibaly I, Loraine AE (2008) CressExpress: a tool for large-scale mining of expression data from Arabidopsis. Plant Physiol 147: 1004-1016
68. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res 34: D535-D539
69. Steinhauser D, Usadel B, Luedemann A, Thimm O, Kopka J (2004) CSB. DB: a comprehensive systems-biology database. Bioinformatics 20: 3647-3651
70. Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK Jr, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, et al (2007) The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol 25: 887-893
71. Toufighi K, Brady SM, Austin R, Ly E, Provart NJ (2005) The Botany Array Resource: e-northerns, expression angling, and promoter analyses. Plant J 43: 153-163
72. Tyler L, Thomas SG, Hu J, Dill A, Alonso JM, Ecker JR, Sun TP (2004) DELLA proteins and gibberellin-regulated seed germination and floral development in Arabidopsis. Plant Physiol 135: 1008-1019
73. 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: 1633-1651
74. Vandepoele K, Quimbaya M, Casneuf T, De Veylder L, Van de Peer Y (2009) Unraveling transcriptional control in Arabidopsis using cisregulatory elements and coexpression networks. Plant Physiol 150: 535-546
75. Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P, et al (2006) The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics 22: 866-873
76. Yu H, Ito T, Zhao Y, Peng J, Kumar P, Meyerowitz EM (2004) Floral homeotic genes are targets of gibberellin signaling in flower development. Proc Natl Acad Sci USA 101: 7827-7832
77. Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W (2004) GENEVESTIGATOR: Arabidopsis microarray database and analysis toolbox. Plant Physiol 136: 2621-2632