Skip to main content
SpringerLink
Log in
Book cover

Computational Intelligence in Bioinformatics pp 237–256Cite as

Saccharomyces pombe and Saccharomyces cerevisiae Gene Regulatory Network Inference Using the Fuzzy Logic Network

  • Chapter

  • 962 Accesses

Part of the book series: Studies in Computational Intelligence ((SCI,volume 94))

Summary

In this chapter, a novel gene regulatory network inference algorithm based on the fuzzy logic network theory is proposed and tested. The key motivation for this algorithm is that genes with regulatory relationships may be modeled via fuzzy logic, and the strength of regulations may be represented as the length of accumulated distance during a period of time intervals. One unique feature of this algorithm is that it makes very limited a priori assumptions concerning the modeling. Hence the algorithm is categorized as a data-driven algorithm. With the theoretical guidelines to quantify the upper limits of parameters, the algorithm is implemented to infer gene regulatory networks for Saccharomyces cerevisiae and Saccharomyces pombe. The computation results not only prove the validity of the data-driven algorithm, but also offer a possible explanation concerning the difference of network stabilities between the budding yeast and the fission yeast.

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

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.00
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

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Strogatz S (2001) Exploring complex networks. Nature 410:268–276

    Article  Google Scholar 

  2. Nachman I, Regev A, Friedman N (2004) Inferring quantitative models of regulatory networks from expression data. Bioinformatics 20:i248–i256

    Article  Google Scholar 

  3. Matsuno H, Doi A, Nagasaki M, Miyano S (2000) Hybrid Petri net representation of gene regulatory network. Pacific Symposium on Biocomputing 5:341–352

    Google Scholar 

  4. TeichMann S, Babu M (2004) Gene regulatory network growth by duplication. Nature Genetics 36:492–496

    Article  Google Scholar 

  5. Sprinzak D, Elowitz M (2005) Reconstruction of genetic circuits. Nature 438:443–448

    Article  Google Scholar 

  6. Ong I, Page D, and Costa V (2006) Inferring Regulatory Networks from Time Series Expression Data and Relational Data via Inductive Logic Programming. In: Proc. 16th International Conference on Inductive Logic Programming, Spain

    Google Scholar 

  7. Kwon A, Hoos H, Ng R (2003) Inference of transcriptional regulation relationships from gene expression data. Bioinformatics 19:905–912

    Article  Google Scholar 

  8. Joseph Z (2004) Analyzing time series gene expression data. Bioinformatics 20:2493–2503

    Article  Google Scholar 

  9. Georgantas R, Tanadve V, Malehorn M, Heimfeld S, Chen C, Carr L, Martinez-Murillo F, Riggins G, Kowalski J, Civin C (2004) Microarray and serial analysis of gene expression analyses indentify known and novel transcripts overexpressed in hematopoietic stem cells. Cancer Research 64:4434–4441

    Article  Google Scholar 

  10. Lee T, Rinaldi N, Robert F, Odom D, Joseph Z, Gerber G, Hannettt N, Harbinson CT, Thompson C.M, Simon I, Zeitlinger J, Jennings E, Murray H, Gordon DB, Ren B, Wyrick J, Tagne J, Volkert T, Fraenkel E, Gifford D, Young R (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298:799–804

    Article  Google Scholar 

  11. Fung E, Thulasiraman V, Weinberger SR, Dalmasso E (2001) Protein biochips for differential profiling. Current Opinion in Biotechnology 12:65–69

    Article  Google Scholar 

  12. Cao Y, Wang P, Tokuta A (2005) 3. In: Gene regulating network discovery. Volume 5 of Studies in Computational Intelligence. Springer-Verlag GmbH 49–78

    Google Scholar 

  13. Woolf P, Wang Y (2000) A fuzzy logic approach to analyzing gene expression data. Physiological Genomics 3:9–15

    Google Scholar 

  14. Cao Y, Wang P, Tokuta A (2006) S. pombe regulatory network construction using the fuzzy logic network. Poster, LSS Computational Systems Bioinformatics Conference, Stanford University

    Google Scholar 

  15. Hajek P (1998) Metamathematics of fuzzy logic. Volume 4 of Trends in Logic. Kluwer academic publishers, Boston

    Google Scholar 

  16. Reiter C (2002) Fuzzy automata and life. Complexity 3:19–29

    Article  MathSciNet  Google Scholar 

  17. Derrida B, Pomeau Y (1986) Random networks of automata: A simple annealed approximation. Europhysics letters 1:45–49

    Article  Google Scholar 

  18. Sole R, Luque B, Kauffman S (2000) Phase transition in random network with multiple states. Technical report, Santa Fe Institute

    Google Scholar 

  19. Resconi G, Cao Y, Wang P (2006) Fuzzy biology. In: Proc. 5th International Symposium on Intelligent Manufacturing Systems, Sajarya, Turkey 29–31

    Google Scholar 

  20. Kauffman S, Peterson C, Samuelsson B, Troein C (2004) Genetic networks with canalyzing Boolean rules are always stable. PNAS 101:17102–17107

    Article  Google Scholar 

  21. Cao Y (2006) Fuzzy Logic Network Theory with Applications to Gene Regulatory Networks. PhD thesis, Duke University

    Google Scholar 

  22. Spellman P, Sherlock G, Zhang M, Iyer V, Anders K, Eisen M, Brown P, Botstein D, Futcher B (1998) Comprehensive identification of cell cycle regulated genes of the yeast saccharomyces cerevisiae by microarray hybridization, molecular biology of the cell. Molecular Biology of the Cell 9:3273–3297

    Google Scholar 

  23. Rustici G, Mata J, Kivinen K, Lio P, Penkett C, Burns G, Hayles J, Brazma A, Nurse P, Bahler J (2004) Periodic gene expression program of the fission yeast cell cycle. Nature genetics 36:809–817

    Article  Google Scholar 

  24. Heckman D, Geiser D, Eidell B, Stauffer R, Kardos N, Hedges S (2001) Molecular evidence for the early colonization of land by fungi and plants. Science 293:1129–1133

    Article  Google Scholar 

  25. Forsburg S (1999) The best yeast. Trends in genetics 15:340–344

    Article  Google Scholar 

  26. Cappellaro C, Baldermann C, Rachel R, Tanner W (1994) Mating type-specific cell-cell recognition of saccharomyces cerevisiae: cell wall attachment and active sites of a- and alpha-agglutinin. EMBO Journal 13:4737–4744

    Google Scholar 

  27. Lockhart S, Zhao R, Daniels K, Soll D (2003) Alpha-pheromone-induced “shmooing” and gene regulation require white-opaque switching during candida albicans mating. Eukaryotic cell 2:847–855

    Article  Google Scholar 

  28. Stone E, Heun P, Laroche T, Pillus L, Gasser S (2000) Map kinase signaling induces nuclear reorganization in budding yeast. Current Biology 10:373–382

    Article  Google Scholar 

  29. Erdman S, Lin L, Malczynski M, Snyder M (1998) Pheromone-regulated genes required for yeast mating differentiation. Journal of Cell Biology 140:461–483

    Article  Google Scholar 

  30. Oehlen L, McKinney J, Cross F (1996) Ste12 and mcm1 regulate cell cycle-dependent transcription of far1. Molecular Cell Biology 16:2830–2837

    Google Scholar 

  31. Jin H, Carlile C, Nolan S, Grote E (2004) Prm1 prevents contact-dependent lysis of yeast mating pairs. Eukaryotic Cell 3:1664–1673

    Article  Google Scholar 

  32. Wang K, Vavassori S, Schweizer L, Schweizer M (2004) Impaired prpp-synthesizing capacity compromises cell integrity signalling in saccharomyces cerevisiae. Microbiology 150:3327–3339

    Article  Google Scholar 

  33. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U (2002) Network motifs: Simple building blocks of complex networks. Science 298:824–827

    Article  Google Scholar 

  34. Shen-Orr S, Milo R, Mangan S, Alon U (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genetics 31:64–68

    Article  Google Scholar 

  35. Thieffry D, Romero D (1999) The modularity of biological regulatory networks. Biosystems 50:49–59

    Article  Google Scholar 

  36. Milo R, Itzkovitz S, Kashtan N, Levitt R, Shen-Orr S, Ayzenshtat I, Sheffer M, Alon U (2004) Superfamilies of evolved and designed networks. Science 303:1538–1542

    Article  Google Scholar 

  37. Thieffry D, Huerta A, Perez-Rueda E, Collado-Vides J (1998) From specific gene regulation to genomic networks: A global analysis of transcriptional regulation in Escherichia coli. BioEssays 20:433–440

    Article  Google Scholar 

  38. Kapteyn J, Montijn R, Vink E, de la Cruz J, Llobell A, Douwes J, Shimoi H, Lipke P, Klis F (1996) Retention of Saccharomyces cerevisiae cell wall proteins through a phosphodiester-linked beta-1,3-/beta-1,6-glucan heteropolymer. Glycobiology 6:337–345

    Article  Google Scholar 

  39. Jacobson E, Meadows R, Measel J (1985) Cell cycle perturbations following DNA damage in the presence of ADP-ribosylation inhibitors. Carcinogenesis 6:711–714

    Article  Google Scholar 

  40. Morris D, Phatnani H, Greenleaf A (1999) Phospho-carboxyl-terminal domain binding and the role of a prolyl isomerase in pre-mRNA 3’-end formation. Journal of Biological Chemistry 274:31583–31587

    Article  Google Scholar 

  41. Richnau N, Aspenstrom P (2001) RICH, a rho GTPase-activating protein domain-containing protein involved in signaling by cdc42 and rac1. Journal of Biological Chemistry 276:35060–35070

    Article  Google Scholar 

  42. Read R, Martinho R, Wang S, Carr A, Norbury C (2002) Cytoplasmic poly(A) polymerases mediate cellular responses to S phase arrest. PNAS 99:12079–12084

    Article  Google Scholar 

  43. Trautwein M, Schindler C, Gauss R, Dengjel J (2006) Arf1p, Chs5p and the CHAPs are required for export of specialized cargo from the Golgi. the EMBO Journal 25:943–954

    Article  Google Scholar 

  44. Lee J, Choi J, Park B, Park Y, Lee M, Park H, Maeng P (2004) Differential expression of the chitin synthase genes of Aspergillus nidulans, chsA, chsB, and chsC, in response to developmentalstatusandenvironmentalfactors.FungalGeneticsandBiology41:635–646

    Google Scholar 

  45. Moussalli M, Pipe S, Hauri H, Nichols W, Ginsburg D, Kauffman R (1999) Mannose-dependent endoplasmic reticulum (ER)-golgi intermediate compartment-53-mediated ER to Golgi trafficking of coagulation factors V and VIII. Journal of Biological Chemistry 274:32539–32542

    Article  Google Scholar 

  46. Chao S, Greenleaf A, Price D (2001) Juglone, an inhibitor of the peptidyl-prolyl isomerase pin1, also directly blocks transcription. Nucleic Acids Research 29:767–773

    Article  Google Scholar 

  47. Mouyna I, Hartland R, Fontaine T, Diaquin M, Simenel C, Delepierre M, Henrissat B, Latge J (1998) A 1,3-beta-glucanosyltransferase isolated from the cell wall of Aspergillus fumigatus is a homologue of the yeast Bgl2p. Microbiology 144:3171–3180

    Article  Google Scholar 

  48. Mosser D, Kotzbauer P, Sarge K, Morimoto R (1990) In vitro activation of heat shock transcription factor DNA-binding by calcium and biochemical conditions that affect protein conformation. PNAS 87:3748–3752

    Article  Google Scholar 

  49. Pierucci O, Rickert M (1985) Duplication of Escherichia coli during inhibition of net phospholipid synthesis. Journal of Bacteriology 162:374–382

    Google Scholar 

  50. Glonek J, Lipinska B, Krzewski K, Zolese G, Bertoli E, Tanfani F (1997) HtrA heat shock protease interacts with phospholipid membranes and undergoes conformational changes. Journal of Biolgocial chemistry 272:8974–8982

    Google Scholar 

  51. Solomon M, Larsen P, Varshavsky A (1988) Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell 53:937–947

    Article  Google Scholar 

  52. Derkx P, Madrid S (2001) The Aspergillus niger cypA gene encodes a cyclophilin that mediates sensitivity to the immunosuppressant cyclosporin A. Molecular Genetics and Genomics 266:527–536

    Article  Google Scholar 

  53. Riou-Khamlichi C, Menges M, Healy J, Murray J (2000) Sugar control of the plant cell cycle: Differential regulation of Arabidopsis D-type cyclin gene expression. Molecular and Cellular Biology 20:4513–4521

    Article  Google Scholar 

  54. Gastaldi G, Cova E, Verri A, Laforenza U, Faelli A, Rindi G (2000) Transport of thiamin in rat renal brush border membrane vesicles. Kidney International 57:2043–2054

    Article  Google Scholar 

  55. Bulik D, Olczak M, Lucero H, Osmond B, Robins P, Specht C (2003) Chitin synthesis in Saccharomyces cerevisiae in response to supplementation of growth medium with glucosamine and cell wall stress. Eukaryotic Cell 2:886–900

    Article  Google Scholar 

  56. Jekely G, Arendt D (2006) Evolution of intraflagellar transport from coated vesicles and autogenous origin of the eukaryotic cilium. BioEssays 28:191–198

    Article  Google Scholar 

  57. Corven E, Os C, Mircheff A (1986) Subcellular distribution of ATP-dependent calcium transport in rat duodenal epithelium. Biochimica et biophysica acta 861:267–276

    Article  Google Scholar 

  58. Levy-Wilson B (1983) Chromatin structure and expression of amylase genes in rat pituitary tumor cells. DNA 2:9–13

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Mathematics and Computer Science, North Carolina Central University, 1801 Fayetteville Street, Durham, NC, 27707

    Yingjun Cao & Alade Tokuta

  2. Department of Electrical and Computer Engineering, Duke University, P.O. Box 90291, Durham, NC, 27708

    Paul P. Wang

Authors
  1. Yingjun Cao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Paul P. Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Alade Tokuta
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Neurology Buffalo Neuroimaging Analysis Center The Jacobs Neurological Institute University at Buffalo, The State University of New York, 100 High Street, Buffalo, NY, 14203, USA

    Arpad Kelemen

  2. Centre for Quantifiable Quality of Service in Communication Systems (Q2S), Centre of Excellence Norwegian University of Science and Technology, O.S. Bragstads plass 2E, N-7491, Trondheim, Norway

    Ajith Abraham

  3. School of Information Science and Engineering, Jinan University, Jiwei Road 106, Jinan, 250022, P.R. China

    Yuehui Chen

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Cao, Y., Wang, P.P., Tokuta, A. (2008). Saccharomyces pombe and Saccharomyces cerevisiae Gene Regulatory Network Inference Using the Fuzzy Logic Network. In: Kelemen, A., Abraham, A., Chen, Y. (eds) Computational Intelligence in Bioinformatics. Studies in Computational Intelligence, vol 94. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-76803-6_10

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-76803-6_10

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-76802-9

  • Online ISBN: 978-3-540-76803-6

  • eBook Packages: EngineeringEngineering (R0)

Publish with us

Policies and ethics

Search

Navigation