Discovering functional modules across diverse maize transcriptomes using COB, the co-expression browser

PLoS ONE

Volumn 9, Issue 6, 2014, Pages

  Schaefer, Robert J ^a   Briskine, Roman ^b   Springer, Nathan M ^c   Myers, Chad L ^a,b  

^a UNIVERSITY OF MINNESOTA   (United States)

^b University of Minnesota   (United States)

^c UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ARTICLE; DATA ANALYSIS SOFTWARE; DATA BASE; GENE CLUSTER; GENE EXPRESSION; GENE FUNCTION; GENE MAPPING; GENE REGULATORY NETWORK; GENE STRUCTURE; GENETIC ASSOCIATION; GENETIC VARIABILITY; INTERNET; MAIZE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENOME; CLUSTER ANALYSIS; GENE EXPRESSION REGULATION; GENE ONTOLOGY; GENETICS; QUANTITATIVE TRAIT LOCUS;

CLUSTER ANALYSIS; GENE EXPRESSION REGULATION, PLANT; GENE ONTOLOGY; GENE REGULATORY NETWORKS; INTERNET; QUANTITATIVE TRAIT LOCI; TRANSCRIPTOME; ZEA MAYS;

EID: 84903388811     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0099193     Document Type: Article

References (45)

1. Wei H, Persson S, Mehta T, Srinivasasainagendra V, Chen L, et al. (2006) Transcriptional coordination of the metabolic network in Arabidopsis. Plant Physiol 142: 762-774. doi:10.1104/pp.106.080358. (Pubitemid 44583145)
2. Myers CL, Robson D, Wible A, Hibbs MA, Chiriac C, et al. (2005) Discovery of biological networks from diverse functional genomic data. Genome Biol 6: R114. doi:10.1186/gb-2005-6-13-r114.
3. Ideker T, Ozier O, Schwikowski B, Andrew F (2002) Discovering regulatory and signalling circuits in molecular interactions networks. Bioinformatics 18: 233-240. doi:10.1093/bioinformatics/18.suppl-1.S233.
4. Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, et al. (2007) Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science 316: 593-597. doi:10.1126/science.1132067. (Pubitemid 46683144)
5. Huttenhower C, Hibbs M, Myers C, Troyanskaya OG (2006) A scalable method for integration and functional analysis of multiple microarray datasets. Bioinformatics 22: 2890-2897. doi:10.1093/bioinformatics/btl492. (Pubitemid 44811560)
6. Moreno-Risueno MA, Busch W, Benfey PN (2010) Omics meet networks - using systems approaches to infer regulatory networks in plants. Curr Opin Plant Biol 13: 126-131. doi:10.1016/j.pbi.2009.11.005.
7. Aoki K, Ogata Y, Shibata D (2007) Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol 48: 381-390. doi:10.1093/pcp/pcm013. (Pubitemid 47355543)
8. Mochida K, Uehara-Yamaguchi Y, Yoshida T, Sakurai T, Shinozaki K (2011) Global landscape of a co-expressed gene network in barley and its application to gene discovery in Triticeae crops. Plant Cell Physiol 52: 785-803. doi:10.1093/pcp/pcr035.
9. Fukushima A, Nishizawa T, Hayakumo M, Hikosaka S, Saito K, et al. (2012) Exploring Tomato Gene Functions Based on Coexpression Modules Using Graph Clustering and Differential Coexpression Approaches. Plant Physiol. doi:10.1104/pp.111.188367.
10. Zhu T, Budworth P, Chen W, Provart N, Chang H-S, et al. (2003) Transcriptional control of nutrient partitioning during rice grain filling. Plant Biotechnol J 1: 59-70. doi:10.1046/j.1467-7652.2003.00006.x.
11. Ficklin SP, Luo F, Feltus FA (2010) The association of multiple interacting genes with specific phenotypes in rice using gene coexpression networks. Plant Physiol 154: 13-24. doi:10.1104/pp.110.159459.
12. Swanson-wagner R, Briskine R, Schaefer R, Hufford MB, Ross-ibarra J (2012) Reshaping of the maize transcriptome by domestication. PNAS 109: 11878-11883. doi:10.1073/pnas.1201961109/-/DCSupplemental.www.pnas.org/cgi/doi/ 10.1073/pnas.1201961109.
13. Downs GS, Bi Y-M, Colasanti J, Wu W, Chen X, et al. (2013) A Developmental Transcriptional Network for Maize Defines Coexpression Modules. Plant Physiol 161: 1830-1843. doi:10.1104/pp.112.213231.
14. Ficklin SP, Feltus FA (2011) Gene Co-Expression Network Alignment and Conservation of Gene Modules Between Two Grass Species: Maize (Zea mays) and Rice (Oryza sativa). Plant Physiol 156: 1244-1256. doi:10.1104/pp.111.173047.
15. Deshpande R, Sharma S, Verfaillie CM, Hu W-S, Myers CL (2010) A scalable approach for discovering conserved active subnetworks across species. PLoS Comput Biol 6: e1001028. doi:10.1371/journal.pcbi.1001028.
16. Baxter I, Ouzzani M, Orcun S, Kennedy B, Jandhyala SS, et al. (2007) Purdue ionomics information management system. An integrated functional genomics platform. Plant Physiol 143: 600-611. doi:10.1104/pp.106.092528. (Pubitemid 46940952)
17. Morrell PL, Buckler ES, Ross-Ibarra J (2011) Crop genomics: advances and applications. Nat Rev Genet 13: 85-96. doi:10.1038/nrg3097.
18. Sekhon RS, Lin H, Childs KL, Hansey CN, Buell CR, et al. (2011) Genomewide atlas of transcription during maize development. Plant J 66: 553-563. doi:10.1111/j.1365-313X.2011.04527.x.
19. Lawrence CJ, Dong Q, Polacco ML, Seigfried TE, Brendel V (2004) MaizeGDB, the community database for maize genetics and genomics. Nucleic Acids Res 32: D393-7. doi:10.1093/nar/gkh011. (Pubitemid 38081683)
20. DAVID FN (1949) The moments of the z and F distributions. Biometrika 36: 394-403. doi: 10.1093/biomet/36.3-4.394.
21. Ghazalpour A, Doss S, Zhang B, Wang S, Plaisier C, et al. (2006) Integrating genetic and network analysis to characterize genes related to mouse weight. PLoS Genet 2: e130. doi:10.1371/journal.pgen.0020130.
22. Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, et al. (2009) Coexpression 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.
23. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32: D258-61. doi:10.1093/nar/gkh036. (Pubitemid 38081651)
24. Usadel B, Poree F, Nagel A, Lohse M, Czedik-Eysenberg A, et al. (2009) A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize. Plant Cell Environ 32: 1211-1229. doi:10.1111/j.1365-3040.2009.01978.x.
25. Orlando DA, Brady SM, Koch JD, Dinneny JR, Benfey PN (2009) Manipulating large-scale Arabidopsis microarray expression data: identifying dominant expression patterns and biological process enrichment. Methods Mol Biol 553: 57-77. doi:10.1007/978-1-60327-563-7-4.
26. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504. doi:10.1101/gr.1239303. (Pubitemid 37428274)
27. Dongen SM van (2001) Graph clustering by flow simulation. PhD thesis, University of Utrecht, May 2000. Available: http://micans.org/mcl/. Accessed 2014 Apr 7.
28. Swanson-Wagner RA, Eichten SR, Kumari S, Tiffin P, Stein JC, et al. (2010) Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Res 20: 1689-1699. doi:10.1101/gr.109165. 110.
29. Myers AM (2000) Recent Progress toward Understanding Biosynthesis of the Amylopectin Crystal. PLANT Physiol 122: 989-998. doi: 10.1104/pp.122.4.989.
30. Fan L, Bao J, Wang Y, Yao J, Gui Y, et al. (2009) Post-domestication selection in the maize starch pathway. PLoS One 4: e7612. doi:10.1371/journal. pone.0007612.
31. Giroux MJ, Boyer C, Feix G, Hannah LC (1994) Coordinated Transcriptional Regulation of Storage Product Genes in the Maize Endosperm. Plant Physiol 106: 713-722.
32. De Sousa SM, Paniago M del G, Arruda P, Yunes JA (2008) Sugar levels modulate sorbitol dehydrogenase expression in maize. Plant Mol Biol 68: 203-213. doi:10.1007/s11103-008-9362-0.
33. Ramirez J, Bolduc N, Lisch D, Hake S (2009) Distal expression of knotted1 in maize leaves leads to reestablishment of proximal/distal patterning and leaf dissection. Plant Physiol 151: 1878-1888. doi:10.1104/pp.109.145920.
34. Bolduc N, Yilmaz A, Mejia-Guerra MK, Morohashi K, O'Connor D, et al. (2012) Unraveling the KNOTTED1 regulatory network in maize meristems. Genes Dev 26: 1685-1690. doi:10.1101/gad.193433.112.
35. Fowler JE, Freeling M (1996) Genetic analysis of mutations that alter cell fates in maize leaves: dominant Liguleless mutations. Dev Genet 18: 198-222. doi:10.1002/(SICI)1520-6408(1996)18:3〈198::AID-DVG2〉3.0.CO;2- 4. (Pubitemid 26136805)
36. Foster T, Yamaguchi J, Wong BC, Veit B, Hake S (1999) Gnarley1 is a dominant mutation in the knox4 homeobox gene affecting cell shape and identity. Plant Cell 11: 1239-1252. doi: 10.2307/3870746.
37. Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q, et al. (2011) Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43: 159-162. doi:10.1038/ng.746.
38. Becraft PW, Freeling M (1994) Genetic Analysis of Rough sheath1 Developmental Mutants of Maize. Genetics 136: 295-311. (Pubitemid 24016694)
39. Kim CY, Bove J, Assmann SM (2008) Overexpression of wound-responsive RNA-binding proteins induces leaf senescence and hypersensitive-like cell death. New Phytol 180: 57-70. doi: 10.1111/j.1469-8137.2008.02557.x.
40. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, et al. (2005) A gene expression map of Arabidopsis thaliana development. Nat Genet 37: 501-506. doi:10.1038/ng1543. (Pubitemid 40617278)
41. Swanson-wagner R, Briskine R, Schaefer R, Hufford MB, Ross-ibarra J (2012) Reshaping of the maize transcriptome by domestication. PNAS 109: 11878-11883. doi:10.1073/pnas.1201961109/-/DCSupplemental.www.pnas.org/cgi/doi/ 10.1073/pnas.1201961109.
42. Sekhon RS, Lin H, Childs KL, Hansey CN, Buell CR, et al. (2011) Genomewide atlas of transcription during maize development. Plant J 66: 553-563. doi:10.1111/j.1365-313X.2011.04527.x.
43. Huttenhower C, Schroeder M, Chikina MD, Troyanskaya OG (2008) The Sleipnir library for computational functional genomics. Bioinformatics 24: 1559-1561. doi: 10.1093/bioinformatics/btn237. (Pubitemid 351911717)
44. Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, et al. (2010) Cytoscape Web: an interactive web-based network browser. Bioinformatics 26: 2347-2348. doi:10.1093/bioinformatics/btq430.
45. Alstott J, Bullmore E, Plenz D (2014) powerlaw: a Python package for analysis of heavy-tailed distributions. PLoS One 9: e85777. doi:10.1371/journal. pone.0085777.