Systems Biology from a Yeast Omics Perspective

Overview

Journal FEBS Lett

Specialty Biochemistry

Date 2009 Nov 12

PMID 19903479

Citations 23

Authors

Michael Snyder

Jennifer E G Gallagher

Affiliations

Soon will be listed here.

Abstract

Systems biology represents a paradigm shift from the study of individual genes, proteins or other components to that of the analysis of entire pathways, cellular, developmental, or organismal processes. Large scale studies, primarily initiated in Saccharomyces cerevisiae, have allowed the identification and characterization of components on an unprecedented level. Large scale interaction, transcription factor binding and phosphorylation data have enabled the elucidation of global regulatory networks. These studies have helped provide an understanding of cellular pathways and processes at a global and systems level.

Citing Articles

scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse.

Huang X, Song C, Zhang G, Li Y, Zhao Y, Zhang Q Nucleic Acids Res. 2023; 52(D1):D293-D303.

PMID: 37889053 PMC: 10767939. DOI: 10.1093/nar/gkad885.

Gene regulatory network inference in the era of single-cell multi-omics.

Badia-I-Mompel P, Wessels L, Muller-Dott S, Trimbour R, Ramirez Flores R, Argelaguet R Nat Rev Genet. 2023; 24(11):739-754.

PMID: 37365273 DOI: 10.1038/s41576-023-00618-5.

Active pharmaceutical ingredient (API) chemicals: a critical review of current biotechnological approaches.

Kumar V, Bansal V, Madhavan A, Kumar M, Sindhu R, Awasthi M Bioengineered. 2022; 13(2):4309-4327.

PMID: 35135435 PMC: 8973766. DOI: 10.1080/21655979.2022.2031412.

Yeast Systems Biology: The Continuing Challenge of Eukaryotic Complexity.

Oliver S Methods Mol Biol. 2019; 2049:3-13.

PMID: 31602602 DOI: 10.1007/978-1-4939-9736-7_1.

Yeast epigenetics: the inheritance of histone modification states.

OKane C, Hyland E Biosci Rep. 2019; 39(5).

PMID: 30877183 PMC: 6504666. DOI: 10.1042/BSR20182006.

References

Burns N, Grimwade B, Choi E, Finberg K, Roeder G, Snyder M . Large-scale analysis of gene expression, protein localization, and gene disruption in Saccharomyces cerevisiae. Genes Dev. 1994; 8(9):1087-105. DOI: 10.1101/gad.8.9.1087. View

Yamada K, Lim J, Dale J, Chen H, Shinn P, Palm C . Empirical analysis of transcriptional activity in the Arabidopsis genome. Science. 2003; 302(5646):842-6. DOI: 10.1126/science.1088305. View

Ni L, Bruce C, Hart C, Leigh-Bell J, Gelperin D, Umansky L . Dynamic and complex transcription factor binding during an inducible response in yeast. Genes Dev. 2009; 23(11):1351-63. PMC: 2701586. DOI: 10.1101/gad.1781909. View

Christie K, Hong E, Cherry J . Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. Trends Microbiol. 2009; 17(7):286-94. PMC: 3057094. DOI: 10.1016/j.tim.2009.04.005. View

Pan X, Ye P, Yuan D, Wang X, Bader J, Boeke J . A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell. 2006; 124(5):1069-81. DOI: 10.1016/j.cell.2005.12.036. View

Giaever G, Chu A, Ni L, Connelly C, Riles L, Veronneau S . Functional profiling of the Saccharomyces cerevisiae genome. Nature. 2002; 418(6896):387-91. DOI: 10.1038/nature00935. View

Tong A, Lesage G, Bader G, Ding H, Xu H, Xin X . Global mapping of the yeast genetic interaction network. Science. 2004; 303(5659):808-13. DOI: 10.1126/science.1091317. View

Reboul J, Vaglio P, Tzellas N, Thierry-Mieg N, Moore T, Jackson C . Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans. Nat Genet. 2001; 27(3):332-6. DOI: 10.1038/85913. View

Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J . Global analysis of protein phosphorylation in yeast. Nature. 2005; 438(7068):679-84. DOI: 10.1038/nature04187. View

10.

Ross-Macdonald P, Coelho P, Roemer T, Agarwal S, Kumar A, Jansen R . Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature. 1999; 402(6760):413-8. DOI: 10.1038/46558. View

11.

Huber A, Bodenmiller B, Uotila A, Stahl M, Wanka S, Gerrits B . Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis. Genes Dev. 2009; 23(16):1929-43. PMC: 2725941. DOI: 10.1101/gad.532109. View

12.

von Mering C, Krause R, Snel B, Cornell M, Oliver S, Fields S . Comparative assessment of large-scale data sets of protein-protein interactions. Nature. 2002; 417(6887):399-403. DOI: 10.1038/nature750. View

13.

Martzen M, McCraith S, Spinelli S, Torres F, Fields S, Grayhack E . A biochemical genomics approach for identifying genes by the activity of their products. Science. 1999; 286(5442):1153-5. DOI: 10.1126/science.286.5442.1153. View

14.

Schuldiner M, Collins S, Thompson N, Denic V, Bhamidipati A, Punna T . Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell. 2005; 123(3):507-19. DOI: 10.1016/j.cell.2005.08.031. View

15.

Holt K . Identifying adaptive differences could provide insight. Nature. 2009; 458(7235):145. DOI: 10.1038/458145b. View

16.

Denison C, Rudner A, Gerber S, Bakalarski C, Moazed D, Gygi S . A proteomic strategy for gaining insights into protein sumoylation in yeast. Mol Cell Proteomics. 2004; 4(3):246-54. DOI: 10.1074/mcp.M400154-MCP200. View

17.

Huh W, Falvo J, Gerke L, Carroll A, Howson R, Weissman J . Global analysis of protein localization in budding yeast. Nature. 2003; 425(6959):686-91. DOI: 10.1038/nature02026. View

18.

Zhu X, Gerstein M, Snyder M . Getting connected: analysis and principles of biological networks. Genes Dev. 2007; 21(9):1010-24. DOI: 10.1101/gad.1528707. View

19.

Holt L, Tuch B, Villen J, Johnson A, Gygi S, Morgan D . Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution. Science. 2009; 325(5948):1682-6. PMC: 2813701. DOI: 10.1126/science.1172867. View

20.

Tarassov K, Messier V, Landry C, Radinovic S, Serna Molina M, Shames I . An in vivo map of the yeast protein interactome. Science. 2008; 320(5882):1465-70. DOI: 10.1126/science.1153878. View