Skip to main content
SpringerLink
Log in

PlaNet: Comparative Co-Expression Network Analyses for Plants

  • Protocol
  • First Online:
Plant Genomics Databases

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1533))

Abstract

Functional relations between genes can be represented as networks. These networks have been successfully used to infer gene function and to mediate transfer of functional knowledge between species. Transcriptionally coordinated or co-expressed genes tend to be functionally related, which combined with availability of transcriptomic data for multiple plant species make the co-expression networks a useful resource for the plant community. In this chapter, we describe PlaNet (www.gene2function.de), a database that includes comparative analyses for co-expression networks of 11 plant species. We exemplify how the tools included in PlaNet can be used to predict gene function, transfer knowledge, and discover conserved and multiplied gene modules.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Rhee SY, Mutwil M (2014) Towards revealing the functions of all genes in plants. Trends Plant Sci 19:212–221

    Article  CAS  PubMed  Google Scholar 

  2. Oliver S (2000) Guilt-by-association goes global. Nature 403:601–603

    Article  CAS  PubMed  Google Scholar 

  3. 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

    Article  CAS  PubMed  Google Scholar 

  4. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800

    Article  Google Scholar 

  5. Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud P-F, Lindquist EA, Kamisugi Y et al (2008) The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319:64–69

    Article  CAS  PubMed  Google Scholar 

  6. Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA et al (2011) The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science 332:960–963

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Vanneste K, Sterck L, Myburg Z, Van de Peer Y, Mizrachi E (2015) Horsetails are ancient polyploids: evidence from Equisetum giganteum. Plant Cell 27:1567. doi:10.1105/tpc.15.00157

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Lee T, Yang S, Kim E, Ko Y, Hwang S, Shin J, Shim JE, Shim H, Kim H, Kim C et al (2015) AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species. Nucleic Acids Res 43:D996–D1002

    Article  PubMed  Google Scholar 

  9. 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

    Article  CAS  PubMed  Google Scholar 

  10. Stuart JM, Segal E, Koller D, Kim SK (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302:249–255

    Article  CAS  PubMed  Google Scholar 

  11. Zarrineh P, Sánchez-Rodríguez A, Hosseinkhan N, Narimani Z, Marchal K, Masoudi-Nejad A (2014) Genome-scale co-expression network comparison across Escherichia coli and Salmonella enterica serovar Typhimurium reveals significant conservation at the regulon level of local regulators despite their dissimilar lifestyles. PLoS One 9:e102871

    Article  PubMed  PubMed Central  Google Scholar 

  12. Gerstein MB, Rozowsky J, Yan K-K, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ et al (2014) Comparative analysis of the transcriptome across distant species. Nature 512:445–448

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Tzfadia O, Amar D, Bradbury LMT, Wurtzel ET, Shamir R (2012) The MORPH algorithm: ranking candidate genes for membership in Arabidopsis and tomato pathways. Plant Cell 24:4389–4406

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Mutwil M, Klie S, Tohge T, Giorgi FM, Wilkins O, Campbell MM, Fernie AR, Usadel B, Nikoloski Z, Persson S (2011) PlaNet: combined sequence and expression comparisons across plant networks derived from seven species. Plant Cell 23:895–910

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Ruprecht C, Mutwil M, Saxe F, Eder M, Nikoloski Z, Persson S (2011) Large-scale co-expression approach to dissect secondary cell wall formation across plant species. Front Plant Sci 2:1–13

    Article  Google Scholar 

  16. Park CY, Wong AK, Greene CS, Rowland J, Guan Y, Bongo LA, Burdine RD, Troyanskaya OG (2013) Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. PLoS Comput Biol 9:e1002957

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Persson S, Wei H, Milne J, Page GP, Somerville CR (2005) Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proc Natl Acad Sci U S A 102:8633–8638

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Ruprecht C, Mendrinna A, Tohge T, Sampathkumar A, Klie S, Fernie AR, Nikoloski Z, Persson S, Mutwil M (2016) FamNet: a framework to identify multiplied modules driving pathway expansion in plants. Plant Physiol 170:1878–1894

    CAS  PubMed  Google Scholar 

  19. Matsuno M, Compagnon V, Schoch GA, Schmitt M, Debayle D, Bassard J-E, Pollet B, Hehn A, Heintz D, Ullmann P et al (2009) Evolution of a novel phenolic pathway for pollen development. Science 325:1688–1692

    Article  CAS  PubMed  Google Scholar 

  20. Kliebenstein DJ (2001) Gene duplication in the diversification of secondary metabolism: tandem 2-oxoglutarate-dependent dioxygenases control glucosinolate biosynthesis in arabidopsis. Plant Cell Online 13:681–693

    Article  CAS  Google Scholar 

  21. Lee I, Seo Y-S, Coltrane D, Hwang S, Oh T, Marcotte EM, Ronald PC (2011) Genetic dissection of the biotic stress response using a genome-scale gene network for rice. Proc Natl Acad Sci U S A 108:18548–18553

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Obayashi T, Nishida K, Kasahara K, Kinoshita K (2011) ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants. Plant Cell Physiol 52:213–219

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. De Bodt S, Hollunder J, Nelissen H, Meulemeester N, Inzé D (2012) CORNET 2.0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations. New Phytol 195:707–720

    Article  PubMed  Google Scholar 

  24. Ficklin SP, Feltus FA (2011) Gene coexpression network alignment and conservation of gene modules between two grass species: maize and rice. Plant Physiol 156:1244–1256

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. 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 Physiol 156:1316–1330

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. McFarlane HE, Döring A, Persson S (2014) The cell biology of cellulose synthesis. Annu Rev Plant Biol 65:69–94

    Article  CAS  PubMed  Google Scholar 

  27. 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 Physiol 158:590–600

    Article  PubMed  Google Scholar 

  28. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A et al (2015) The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 44:D279–D285

    Article  PubMed  PubMed Central  Google Scholar 

  29. Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD (2010) Cytoscape Web: an interactive web-based network browser. Bioinformatics 26:2347–2348

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Hansen BO, Vaid N, Musialak-Lange M, Janowski M, Mutwil M (2014) Elucidating gene function and function evolution through comparison of co-expression networks of plants. Front Plant Sci 5:1–9

    Article  Google Scholar 

  31. Heyndrickx KS, Vandepoele K (2012) Systematic identification of functional plant modules through the integration of complementary data sources. Plant Physiol 159:884–901

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Bringmann M, Li E, Sampathkumar A, Kocabek T, Hauser M-T, Persson S (2012) POM-POM2/cellulose synthase interacting1 is essential for the functional association of cellulose synthase and microtubules in Arabidopsis. Plant Cell 24:163–177

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Endler A, Kesten C, Schneider R, Zhang Y, Ivakov A, Froehlich A, Funke N, Persson S (2015) A mechanism for sustained cellulose synthesis during salt stress. Cell 162:1353–1364

    Article  CAS  PubMed  Google Scholar 

  34. Sterck L, Rombauts S, Vandepoele K, Van De Peer Y, Rouze P, Rouzé P, Van de Peer Y (2007) How many genes are there in plants (… why are they there)? Curr Opin Plant Biol 10:199–203

    Article  CAS  PubMed  Google Scholar 

  35. De Smet R, Van de Peer Y (2012) Redundancy and rewiring of genetic networks following genome-wide duplication events. Curr Opin Plant Biol 15:168–176

    Article  PubMed  Google Scholar 

  36. Persson S, Caffall KH, Freshour G, Hilley MT, Bauer S, Poindexter P, Hahn MG, Mohnen D, Somerville C (2007) The Arabidopsis irregular xylem8 mutant is deficient in glucuronoxylan and homogalacturonan, which are essential for secondary cell wall integrity. Plant Cell 19:237–255

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P et al (2012) ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res 22:1813–1831

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Mortimer JC, Miles GP, Brown DM, Zhang Z, Segura MP, Weimar T, Yu X, Seffen KA, Stephens E, Turner SR et al (2010) Absence of branches from xylan in Arabidopsis gux mutants reveals potential for simplification of lignocellulosic biomass. Proc Natl Acad Sci U S A 107:17409–17414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Pourcel L, Routaboul J-M, Kerhoas L, Caboche M, Lepiniec L, Debeaujon I (2005) TRANSPARENT TESTA10 encodes a laccase-like enzyme involved in oxidative polymerization of flavonoids in Arabidopsis seed coat. Plant Cell 17:2966–2980

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Kitamura S, Oono Y, Narumi I (2016) Arabidopsis pab1, a mutant with reduced anthocyanins in immature seeds from banyuls, harbors a mutation in the MATE transporter FFT. Plant Mol Biol 90:7–18

    Article  CAS  PubMed  Google Scholar 

  42. Sharan R, Ulitsky I, Shamir R (2007) Network-based prediction of protein function. Mol Syst Biol 3:88

    Article  PubMed  PubMed Central  Google Scholar 

  43. Pavlopoulos GA, Secrier M, Moschopoulos CN, Soldatos TG, Kossida S, Aerts J, Schneider R, Bagos PG (2011) Using graph theory to analyze biological networks. BioData Min 4:10

    Article  PubMed  PubMed Central  Google Scholar 

  44. Mutwil M, Usadel B, Schütte M, Loraine A, Ebenhöh O, Persson S (2010) Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm. Plant Physiol 152:29–43

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Lee I, Ambaru B, Thakkar P, Marcotte EM, Rhee SY (2010) Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat Biotechnol 28:149–156

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany

    Sebastian Proost & Marek Mutwil

Authors
  1. Sebastian Proost
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Marek Mutwil
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Marek Mutwil .

Editor information

Editors and Affiliations

  1. PRI Bioscience, Biometris and Bioinformatics, Wageningen University & Research Wageningen, Wageningen, The Netherlands

    Aalt D.J van Dijk

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media New York

About this protocol

Cite this protocol

Proost, S., Mutwil, M. (2017). PlaNet: Comparative Co-Expression Network Analyses for Plants. In: van Dijk, A. (eds) Plant Genomics Databases. Methods in Molecular Biology, vol 1533. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6658-5_12

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-6658-5_12

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6656-1

  • Online ISBN: 978-1-4939-6658-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation