Comparative co-expression analysis in plant biology

Plant, Cell and Environment

Volumn 35, Issue 10, 2012, Pages 1787-1798

  Movahedi, Sara ^a,b   Van Bel, Michiel ^a,b   Heyndrickx, Ken S ^a,b   Vandepoele, Klaas ^a,b  

^a DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^b GHENT UNIVERSITY   (Belgium)

Author keywords

Bioinformatics; Comparative genomics; Expression analysis; Orthology

Indexed keywords

TRANSCRIPTOME;

BIOINFORMATICS; COMPARATIVE STUDY; FUTURE PROSPECT; GENE EXPRESSION; GENOMICS; HOMOLOGY; PHENOTYPE; PLANT; PROTEIN;

ARTICLE; BIOLOGY; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; METHODOLOGY; MULTIGENE FAMILY; PLANT; PLANT GENOME;

COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE REGULATORY NETWORKS; GENOME, PLANT; MULTIGENE FAMILY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANTS; TRANSCRIPTOME;

EID: 84865864061     PISSN: 01407791     EISSN: 13653040     Source Type: Journal    
DOI: 10.1111/j.1365-3040.2012.02517.x     Document Type: Article

References (69)

1. Barrett T. & Edgar R. (2006) Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Methods in Enzymology 411, 352-369.
2. Ben-Dor A., Shamir R. & Yakhini Z. (1999) Clustering gene expression patterns. Journal of Computational Biology 6, 281-297.
3. Benedito V.A., Torres-Jerez I., Murray J.D., etal. (2008) A gene expression atlas of the model legume Medicago truncatula. The Plant Journal 55, 504-513.
4. Bergmann S., Ihmels J. & Barkai N. (2004) Similarities and differences in genome-wide expression data of six organisms. PLoS Biology 2, E9.
5. Chikina M.D. & Troyanskaya O.G. (2011) Accurate quantification of functional analogy among close homologs. PLoS Computational Biology 7, e1001074.
6. D'Haeseleer P. (2005) How does gene expression clustering work? Nature Biotechnology 23, 1499-1501.
7. De Bodt S., Carvajal D., Hollunder J., Van den Cruyce J., Movahedi S. & Inze D. (2010) CORNET: a user-friendly tool for data mining and integration. Plant Physiology 152, 1167-1179.
8. Druka A., Muehlbauer G., Druka I., etal. (2006) An atlas of gene expression from seed to seed through barley development. Functional and Integrative Genomics 6, 202-211.
9. Edwards K.D., Bombarely A., Story G.W., Allen F., Mueller L.A., Coates S.A. & Jones L. (2010) TobEA: an atlas of tobacco gene expression from seed to senescence. BMC Genomics 11, 142.
10. Ficklin S.P. & Feltus F.A. (2011) Gene coexpression network alignment and conservation of gene modules between two grass species: maize and rice. Plant Physiology 156, 1244-1256.
11. Fierro A.C., Vandenbussche F., Engelen K., Van de Peer Y. & Marchal K. (2008) Meta analysis of gene expression data within and across species. Current Genomics 9, 525-534.
12. Finn R.D., Mistry J., Tate J., etal. (2010) The Pfam protein families database. Nucleic Acids Research 38, D211-D222.
13. Gong Q., Li P., Ma S., Indu Rupassara S. & Bohnert H.J. (2005) Salinity stress adaptation competence in the extremophile Thellungiella halophila in comparison with its relative Arabidopsis thaliana. The Plant Journal 44, 826-839.
14. Gregory B.D., Yazaki J. & Ecker J.R. (2008) Utilizing tiling microarrays for whole-genome analysis in plants. The Plant Journal 53, 636-644.
15. Hammond J.P., Broadley M.R., Craigon D.J., Higgins J., Emmerson Z.F., Townsend H.J., White P.J. & May S.T. (2005) Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species. Plant Methods 1, 10.
16. Hardiman G. (2004) Microarray platforms - comparisons and contrasts. Pharmacogenomics 5, 487-502.
17. Hardison R.C. (2003) Comparative genomics. PLoS Biology 1, E58.
18. Huang da W., Sherman B.T. & Lempicki R.A. (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Research 37, 1-13.
19. Humphry M., Bednarek P., Kemmerling B., etal. (2010) A regulon conserved in monocot and dicot plants defines a functional module in antifungal plant immunity. Proceedings of the National Academy of Sciences of the United States of America 107, 21896-21901.
20. Irizarry R.A., Hobbs B., Collin F., Beazer-Barclay Y.D., Antonellis K.J., Scherf U. & Speed T.P. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4, 249-264.
21. Jaiswal P., Avraham S., Ilic K., etal. (2005) Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages. Comparative and Functional Genomics 6, 388-397.
22. Jiao Y., Ma L., Strickland E. & Deng X.W. (2005) Conservation and divergence of light-regulated genome expression patterns during seedling development in rice and Arabidopsis. The Plant Cell 17, 3239-3256.
23. Jiao Y., Tausta S.L., Gandotra N., etal. (2009) A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nature Genetics 41, 258-263.
24. Jupiter D., Chen H. & VanBuren V. (2009) STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data. BMC Bioinformatics 10, 332.
25. Kanehisa M., Goto S., Furumichi M., Tanabe M. & Hirakawa M. (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Research 38, D355-D360.
26. Koonin E.V. (2005) Orthologs, paralogs, and evolutionary genomics. Annual Review of Genetics 39, 309-338.
27. Kuzniar A., van Ham R.C., Pongor S. & Leunissen J.A. (2008) The quest for orthologs: finding the corresponding gene across genomes. Trends in Genetics 24, 539-551.
28. Langfelder P. & Horvath S. (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9, 559.
29. Li L., Stoeckert C.J., Jr & Roos D.S. (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Research 13, 2178-2189.
30. Libault M., Farmer A., Joshi T., Takahashi K., Langley R.J., Franklin L.D., He J., Xu D., May G. & Stacey G. (2010) An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. The Plant Journal 63, 86-99.
31. Lu Y., Huggins P. & Bar-Joseph Z. (2009) Cross species analysis of microarray expression data. Bioinformatics 25, 1476-1483.
32. Luo F., Yang Y., Zhong J., Gao H., Khan L., Thompson D.K. & Zhou J. (2007) Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory. BMC Bioinformatics 8, 299.
33. Lyons E., Pedersen B., Kane J., etal. (2008) Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiology 148, 1772-1781.
34. Ma L., Chen C., Liu X., etal. (2005) A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Research 15, 1274-1283.
35. Martinez M. (2011) Plant protein-coding gene families: emerging bioinformatics approaches. Trends in Plant Science 16, 558-567.
36. Movahedi S., Van de Peer Y. & Vandepoele K. (2011) Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice. Plant Physiology 156, 1316-1330.
37. Mustroph A., Lee S.C., Oosumi T., Zanetti M.E., Yang H., Ma K., Yaghoubi-Masihi A., Fukao T. & Bailey-Serres J. (2010) Cross-kingdom comparison of transcriptomic adjustments to low-oxygen stress highlights conserved and plant-specific responses. Plant Physiology 152, 1484-1500.
38. Mutwil M., Usadel B., Schutte M., Loraine A., Ebenhoh O. & Persson S. (2010) Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm. Plant Physiology 152, 29-43.
39. Mutwil M., Klie S., Tohge T., Giorgi F.M., Wilkins O., Campbell M.M., Fernie A.R., Usadel B., Nikoloski Z. & Persson S. (2011) PlaNet: combined sequence and expression comparisons across plant networks derived from seven species. The Plant Cell 23, 895-910.
40. Ogata Y., Sakurai N., Suzuki H., Aoki K., Saito K. & Shibata D. (2009) The prediction of local modular structures in a co-expression network based on gene expression datasets. Genome Inform 23, 117-127.
41. Ogata Y., Suzuki H., Sakurai N. & Shibata D. (2010) CoP: a database for characterizing co-expressed gene modules with biological information in plants. Bioinformatics 26, 1267-1268.
42. Ostlund G., Schmitt T., Forslund K., Kostler T., Messina D.N., Roopra S., Frings O. & Sonnhammer E.L. (2010) InParanoid 7: new algorithms and tools for eukaryotic orthology analysis. Nucleic Acids Research 38, D196-D203.
43. Parkinson H., Sarkans U., Kolesnikov N., etal. (2011) ArrayExpress update - an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Research 39, D1002-D1004.
44. Proost S., Van Bel M., Sterck L., Billiau K., Van Parys T., Van de Peer Y. & Vandepoele K. (2009) PLAZA: a comparative genomics resource to study gene and genome evolution in plants. The Plant Cell 21, 3718-3731.
45. Quackenbush J. (2002) Microarray data normalization and transformation. Nature Genetics 32 (Suppl), 496-501.
46. Sayers E.W., Barrett T., Benson D.A., etal. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 39, D38-D51.
47. Schmid M., Davison T.S., Henz S.R., Pape U.J., Demar M., Vingron M., Scholkopf B., Weigel D. & Lohmann J.U. (2005) A gene expression map of Arabidopsis thaliana development. Nature Genetics 37, 501-506.
48. Smoot M.E., Ono K., Ruscheinski J., Wang P.L. & Ideker T. (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27, 431-432.
49. Street N.R., Sjodin A., Bylesjo M., Gustafsson P., Trygg J. & Jansson S. (2008) A cross-species transcriptomics approach to identify genes involved in leaf development. BMC Genomics 9, 589.
50. Stuart J.M., Segal E., Koller D. & Kim S.K. (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302, 249-255.
51. Taji T., Seki M., Satou M., Sakurai T., Kobayashi M., Ishiyama K., Narusaka Y., Narusaka M., Zhu J.K. & Shinozaki K. (2004) Comparative genomics in salt tolerance between Arabidopsis and aRabidopsis-related halophyte salt cress using Arabidopsis microarray. Plant Physiology 135, 1697-1709.
52. Takahashi N., Quimbaya M., Schubert V., Lammens T., Vandepoele K., Schubert I., Matsui M., Inze D., Berx G. & De Veylder L. (2010) The MCM-binding protein ETG1 aids sister chromatid cohesion required for postreplicative homologous recombination repair. PLoS Genetics 6, e1000817.
53. Tarazona S., Garcia-Alcalde F., Dopazo J., Ferrer A. & Conesa A. (2011) Differential expression in RNA-seq: a matter of depth. Genome Research 21, 2213-2223.
54. Tirosh I., Bilu Y. & Barkai N. (2007) Comparative biology: beyond sequence analysis. Current Opinion in Biotechnology 18, 371-377.
55. Tsesmetzis N., Couchman M., Higgins J., etal. (2008) Arabidopsis reactome: a foundation knowledgebase for plant systems biology. The Plant Cell 20, 1426-1436.
56. Usadel B., Obayashi T., Mutwil M., Giorgi F.M., Bassel G.W., Tanimoto M., Chow A., Steinhauser D., Persson S. & Provart N.J. (2009a) Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant, Cell & Environment 32, 1633-1651.
57. Usadel B., Poree F., Nagel A., Lohse M., Czedik-Eysenberg A. & Stitt M. (2009b) A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize. Plant, Cell & Environment 32, 1211-1229.
58. Van Bel M., Proost S., Wischnitzki E., Movahedi S., Scheerlinck C., Van de Peer Y. & Vandepoele K. (2012) Dissecting plant genomes with the PLAZA comparative genomics platform. Plant Physiology 158, 590-600.
59. Van de Peer Y., Fawcett J.A., Proost S., Sterck L. & Vandepoele K. (2009) The flowering world: a tale of duplications. Trends in Plant Science 14, 680-688.
60. Vandenbroucke K., Robbens S., Vandepoele K., Inze D., Van de Peer Y. & Van Breusegem F. (2008) Hydrogen peroxide-induced gene expression across kingdoms: a comparative analysis. Molecular Biology and Evolution 25, 507-516.
61. Vandepoele K. & Van de Peer Y. (2005) Exploring the plant transcriptome through phylogenetic profiling. Plant Physiology 137, 31-42.
62. Vandepoele K., Vlieghe K., Florquin K., Hennig L., Beemster G.T., Gruissem W., Van de Peer Y., Inze D. & De Veylder L. (2005) Genome-wide identification of potential plant E2F target genes. Plant Physiology 139, 316-328.
63. Vandepoele K., Quimbaya M., Casneuf T., De Veylder L. & Van de Peer Y. (2009) Unraveling transcriptional control in Arabidopsis using cis-regulatory elements and coexpression networks. Plant Physiology 150, 535-546.
64. Wang L., Xie W., Chen Y., etal. (2010) A dynamic gene expression atlas covering the entire life cycle of rice. The Plant Journal 61, 752-766.
65. Weber M., Harada E., Vess C., Roepenack-Lahaye E. & Clemens S. (2004) Comparative microarray analysis of Arabidopsis thaliana and Arabidopsis halleri roots identifies nicotianamine synthase, a ZIP transporter and other genes as potential metal hyperaccumulation factors. The Plant Journal 37, 269-281.
66. Wise R.P., Caldo R.A., Hong L., Shen L., Cannon E. & Dickerson J.A. (2007) BarleyBase/PLEXdb. Methods in Molecular Biology 406, 347-363.
67. Xu R. & Wunsch D., 2nd (2005) Survey of clustering algorithms. IEEE Transactions on Neural Networks 16, 645-678.
68. Zarrineh P., Fierro A.C., Sanchez-Rodriguez A., De Moor B., Engelen K. & Marchal K. (2011) COMODO: an adaptive coclustering strategy to identify conserved coexpression modules between organisms. Nucleic Acids Research 39, e41.
69. Zimmermann P., Schildknecht B., Craigon D., etal. (2006) MIAME/plant - adding value to plant microarrray experiments. Plant Methods 2, 1.