The bio-analytic resource for plant biology

Methods in Molecular Biology

Volumn 1533, Issue , 2017, Pages 119-148

  Waese, Jamie ^a   Provart, Nicholas J ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

Bioinformatics; Coexpression; EFP; Functional classification; Functional genomics; Hypothesis generation; In silico; Promoter analysis; Protein protein interactions; Proteomics; Subcellular localization; Transcriptomics; Translational biology

Indexed keywords

PROTEOME; TRANSCRIPTOME;

ABIOTIC STRESS; AMINO ACID SEQUENCE; ARABIDOPSIS THALIANA; BARLEY; BARREL MEDIC; BIOINFORMATICS; BIOLOGY; CONSENSUS SEQUENCE; DNA SEQUENCE; GENE EXPRESSION; MAIZE; NONHUMAN; PHENOTYPE; PHYLOGENETIC TREE; PLANT; PLEIOTROPY; POTATO; PREDICTION; PROMOTER REGION; PROTEIN PROTEIN INTERACTION; RICE; SOYBEAN; TOMATO; TRITICALE; COMPUTER INTERFACE; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; GENOMICS; METABOLISM; PROCEDURES; PROTEOMICS; SOFTWARE; WEB BROWSER;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION REGULATION, PLANT; GENOMICS; PLANTS; PROTEOMICS; SOFTWARE; USER-COMPUTER INTERFACE; WEB BROWSER;

EID: 85007232656     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-6658-5_6     Document Type: Chapter

References (53)

1. de Lucas M, Provart NJ, Brady SM (2014) Bioinformatic tools in arabidopsis research. In: Arabidopsis protocols. Springer, New York, NY, pp 97-136
2. Toufighi K, Brady SM, Austin R et al (2005) The botany array resource: e-northerns, expression angling, and promoter analyses. Plant J 43:153-163.doi:10.1111/j.1365-313X.2005.02437.x
3. Winter D, Vinegar B, Nahal H et al (2007) An “Electronic Fluorescent Pictograph” browser for exploring and analyzing large-scale biological data sets. PLoS One 2:e718
4. Wang L, Czedik-Eysenberg A, Mertz RA et al (2014) Comparative analyses of C4 and C3 photosynthesis in developing leaves of maize and rice. Nat Biotechnol 32:1158-1165.doi:10.1038/nbt.3019
5. Patel RV, Nahal HK, Breit R, Provart NJ (2012) BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species. Plant J 71:1038-1050.doi:10.1111/j.1365-313X.2012.05055.x
6. Finkelstein RR, Somerville CR (1990) Three classes of abscisic acid (ABA)-insensitive mutations of arabidopsis define genes that control overlapping subsets of ABA responses. Plant Physiol 94:1172-1179
7. Brady SM, Provart NJ (2009) Web-queryable large-scale data sets for hypothesis generation in plant biology. Plant Cell 21:1034-1051.doi:10.1105/tpc.109.066050
8. Usadel B, Obayashi T, Mutwil M et al (2009) Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant Cell Environ 32:1633-1651.doi:10.1111/j.1365-3040.2009.02040.x
9. Schmid M, Davison TS, Henz SR et al (2005) A gene expression map of Arabidopsis thaliana development. Nat Genet 37:501-506.doi:10.1038/ng1543
10. Nakabayashi K, Okamoto M, Koshiba T et al (2005) Genome-wide profiling of stored mRNA in Arabidopsis thaliana seed germination: epigenetic and genetic regulation of transcription in seed. Plant J Cell Mol Biol 41:697-709.doi:10.1111/j.1365-313X.2005.02337.x
11. Brady SM, Sarkar SF, Bonetta D, McCourt P (2003) The ABSCISIC ACID INSENSITIVE 3 (ABI3) gene is modulated by farnesylation and is involved in auxin signaling and lateral root development in Arabidopsis. Plant J 34:67-75.doi:10.1046/j.1365-313X.2003.01707.x
12. Laubinger S, Zeller G, Henz SR et al (2008) At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana. Genome Biol 9:R112.doi:10.1186/gb-2008-9-7-r112
13. Zeller G, Henz SR, Widmer CK et al (2009) Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays. Plant J 58:1068-1082.doi:10.1111/j.1365-313X.2009.03835.x
14. Brady SM, Orlando DA, Lee J-Y et al (2007) A high-resolution root spatiotemporal map reveals dominant expression patterns. Science 318:801-806.doi:10.1126/science.1146265
15. Haslekås C, Grini PE, Nordgard SH et al (2003) ABI3 mediates expression of the peroxiredoxin antioxidant AtPER1 gene and induction by oxidative stress. Plant Mol Biol 53:313-326
16. Ashburner M, Ball CA, Blake JA et al (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25-29.doi:10.1038/75556
17. Du Z, Zhou X, Ling Y et al (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38:W64-W70.doi:10.1093/nar/gkq310
18. Carbon S, Ireland A, Mungall CJ et al (2009) AmiGO: online access to ontology and annotation data. Bioinformatics 25:288-289.doi:10.1093/bioinformatics/btn615
19. Provart N, Zhu T (2003) A browser-based functional classification SuperViewer for Arabidopsis genomics. Curr Comput Mol Biol 2003:271-272
20. Thimm O, Bläsing O, Gibon Y et al (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J Cell Mol Biol 37:914-939
21. Cui L, Wall PK, Leebens-Mack JH et al (2006) Widespread genome duplications throughout the history of flowering plants. Genome Res 16:738-749.doi:10.1101/gr.4825606
22. Li L, Stoeckert CJ, Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13:2178-2189.doi:10.1101/gr.1224503
23. Johnson D (2013) Examining the regulation of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase in the arabidopsis thaliana shikimate pathway. MSc, University of Toronto
24. Wilkins O, Nahal H, Foong J et al (2009) Expansion and diversification of the Populus R2R3-MYB family of transcription factors. Plant Physiol 149:981-993
25. Heazlewood JL, Verboom RE, Tonti-Filippini J et al (2007) SUBA: the arabidopsis subcellular database. Nucleic Acids Res 35:D213-D218.doi:10.1093/nar/gkl863
26. Geisler-Lee J, O’Toole N, Ammar R et al (2007) A predicted interactome for Arabidopsis. Plant Physiol 145:317-329.doi:10.1104/pp.107.103465
27. Klopffleisch K, Phan N, Augustin K et al (2011) Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis. Mol Syst Biol 7:532.doi:10.1038/msb.2011.66
28. Nakamura S, Lynch TJ, Finkelstein RR (2001) Physical interactions between ABA response loci of Arabidopsis. Plant J 26:627-635
29. Waese J, Pasha A, Wang TT, et al (2016) Gene Slider: sequence logo interactive data-visualization for education and research. Bioinformatics, accepted.doi:10.1093/bioinformatics/btw525
30. Haudry A, Platts AE, Vello E et al (2013) An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet 45:891-898.doi:10.1038/ng.2684
31. Schneider TD, Stephens RM (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18:6097-6100
32. Mathelier A, Zhao X, Zhang AW et al (2014) JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res 42:D142-D147.doi:10.1093/nar/gkt997
33. Weirauch MT, Yang A, Albu M et al (2014) Determination and inference of eukaryotic transcription factor sequence specificity. Cell 158:1431-1443.doi:10.1016/j.cell.2014.08.009
34. Grant CE, Bailey TL, Noble WS (2011) FIMO: scanning for occurrences of a given motif. Bioinformatics 27:1017-1018.doi:10.1093/bioinformatics/btr064
35. Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27:297-300
36. AAustin RS, Hiu S, Waese J, et al (2016) New BAR Tools for Mining Expression Data and Exploring Cis-Elements inArabidopsis thaliana. Plant Journal, aceepted.doi:10.1111/tpj.13261
37. Joshi HJ, Hirsch-Hoffmann M, Baerenfaller K et al (2011) MASCP gator: an aggregation portal for the visualization of arabidopsis proteomics data. Plant Physiol 155:259-270.doi:10.1104/pp.110.168195
38. Kelley LA, Mezulis S, Yates CM et al (2015) The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 10:845-858.doi:10.1038/nprot.2015.053
39. Krishnakumar V, Hanlon MR, Contrino S et al (2015) Araport: the Arabidopsis information portal. Nucleic Acids Res 43:D1003-D1009.doi:10.1093/nar/gku1200
40. Schones DE, Smith AD, Zhang MQ (2007) Statistical significance of cis-regulatory modules. BMC Bioinformatics 8:19.doi:10.1186/1471-2105-8-19
41. Lloyd J, Meinke D (2012) A comprehensive dataset of genes with a loss-of-function mutant phenotype in arabidopsis1[W][OA]. Plant Physiol 158:1115-1129.doi:10.1104/pp.111.192393
42. Tufte ER, Graves-Morris PR (1983) The visual display of quantitative information. Graphics Press, Cheshire, CT
43. Dean G, Cao Y, Xiang D et al (2011) Analysis of gene expression patterns during seed coat development in arabidopsis. Mol Plant 4:1074-1091.doi:10.1093/mp/ssr040
44. Wilkins O, Waldron L, Nahal H et al (2009) Genotype and time of day shape the Populus drought response. Plant J 60:703-715.doi:10.1111/j.1365-313X.2009.03993.x
45. Champigny MJ, Sung WW, Catana V et al (2013) RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions. BMC Genomics 14:578.doi:10.1186/1471-2164-14-578
46. Li P, Ponnala L, Gandotra N et al (2010) The developmental dynamics of the maize leaf transcriptome. Nat Genet 42:1060-1067.doi:10.1038/ng.703
47. Tran F, Penniket C, Patel RV et al (2013) Developmental transcriptional profiling reveals key insights into Triticeae reproductive development. Plant J 74:971-988.doi:10.1111/tpj.12206
48. Ortiz-Ramírez C, Hernandez-Coronado M, Thamm A et al (2016) A transcriptome atlas of Physcomitrella patens provides insights into the evolution and development of land plants. Mol Plant 9:205.doi:10.1016/j.molp.2015.12.002
49. Ho C-L, Wu Y, Shen H et al (2012) A predicted protein interactome for rice. Rice 5:15.doi:10.1186/1939-8433-5-15
50. Austin RS, Vidaurre D, Stamatiou G et al (2011) Next-generation mapping of Arabidopsis genes. Plant J 67:715-725.doi:10.1111/j.1365-313X.2011.04619.x
51. Ilic K, Berleth T, Provart NJ (2004) BlastDigester-a web-based program for efficient CAPS marker design. Trends Genet 20:280-283.doi:10.1016/j.tig.2004.04.012
52. Taylor J, Provart NJ (2006) CapsID: a web-based tool for developing parsimonious sets of CAPS molecular markers for genotyping. BMC Genet 7:27.doi:10.1186/1471-2156-7-27
53. Provart NJ, Alonso J, Assmann SM et al (2016) 50 years of Arabidopsis research: highlights and future directions. New Phytol 209:921-944.doi:10.1111/nph.13687