Natural selection governs local, but not global, evolutionary gene coexpression networks in Caenorhabditis elegans

BMC Systems Biology

Volumn 2, Issue , 2008, Pages

  Jordan, I King ^a   Katz, Lee S ^a   Denver, Dee R ^b   Streelman, J Todd ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^b OREGON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CAENORHABDITIS ELEGANS;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CAENORHABDITIS ELEGANS; DNA MICROARRAY; GENE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETIC SELECTION; GENETICS; MOLECULAR EVOLUTION; MUTATION; PHYSIOLOGY; STATISTICAL MODEL; THEORETICAL MODEL;

ANIMALS; CAENORHABDITIS ELEGANS; DATABASES, GENETIC; EVOLUTION, MOLECULAR; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENES, HELMINTH; MODELS, GENETIC; MODELS, STATISTICAL; MODELS, THEORETICAL; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SELECTION (GENETICS);

EID: 57649177794     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-2-96     Document Type: Article

References (24)

1. Gu Z Nicolae D Lu HH Li WH Rapid divergence in expression between duplicate genes inferred from microarray data Trends Genet 2002, 18:609-613 10.1016/S0168-9525(02)02837-8 12446139
2. Luscombe NM Babu MM Yu H Snyder M Teichmann SA Gerstein M Genomic analysis of regulatory network dynamics reveals large topological changes Nature 2004, 431:308-312 10.1038/nature02782 15372033
3. Makova KD Li WH Divergence in the spatial pattern of gene expression between human duplicate genes Genome Res 2003, 13:1638-1645 403737 12840042 10.1101/gr.1133803
4. Agrawal H Extreme self-organization in networks constructed from gene expression data Phys Rev Lett 2002, 89:268702 10.1103/ PhysRevLett.89.268702 12484863
5. Bergmann S Ihmels J Barkai N Similarities and differences in genome-wide expression data of six organisms PLoS Biol 2004, 2:E9 300882 14737187 10.1371/journal.pbio.0020009
6. Tsaparas P Marino-Ramirez L Bodenreider O Koonin EV Jordan IK Global similarity and local divergence in human and mouse gene co-expression networks BMC Evol Biol 2006, 6:70 1601971 16968540 10.1186/1471-2148-6-70
7. Barabasi AL Oltvai ZN Network biology: Understanding the cell's functional organization Nat Rev Genet 2004, 5:101-113 10.1038/nrg1272 14735121
8. Keller EF Revisiting "scale-free" networks Bioessays 2005, 27:1060-1068 10.1002/bies.20294 16163729
9. Denver DR Morris K Streelman JT Kim SK Lynch M Thomas WK The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans Nat Genet 2005, 37:544-548 10.1038/ng1554 15852004
10. Vassilieva LL Hook AM Lynch M The fitness effects of spontaneous mutations in Caenorhabditis elegans Evolution 2000, 54(4):1234-1246 11005291
11. Jordan IK Marino-Ramirez L Koonin EV Evolutionary significance of gene expression divergence Gene 2005, 345:119-126 1859841 15716085 10.1016/ j.gene.2004.11.034
12. Jordan IK Marino-Ramirez L Wolf YI Koonin EV Conservation and coevolution in the scale-free human gene coexpression network Mol Biol Evol 2004, 21:2058-2070 10.1093/molbev/msh222 15282333
13. Liao BY Zhang J Evolutionary conservation of expression profiles between human and mouse orthologous genes Mol Biol Evol 2006, 23:530-540 10.1093/ molbev/msj054 16280543
14. Rifkin SA Houle D Kim J White KP A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression Nature 2005, 438:220-223 10.1038/nature04114 16281035
15. Dunne JA Williams RJ Martinez ND Network structure and biodiversity loss in food webs: Robustness increases with connectance Ecology Letters 2002, 5
16. Montoya JM Pimm SL Sole RV Ecological networks and their fragility Nature 2006, 442:259-264 10.1038/nature04927 16855581
17. Kim SK Lund J Kiraly M Duke K Jiang M Stuart JM Eizinger A Wylie BN Davidson GS A gene expression map for Caenorhabditis elegans Science 2001, 293:2087-2092 10.1126/science.1061603 11557892
18. Barabasi AL Linked: The new science of networks Cambridge: Perseus 2002
19. Wolf YI Karev G Koonin EV Scale-free networks in biology: New insights into the fundamentals of evolution? Bioessays 2002, 24:105-109 10.1002/ bies.10059 11835273
20. Lun L David A Walter W John D A first-principles approach to understanding the internet's router-level topology Proceedings of the 2004 conference on Applications, technologies, architectures, and protocols for computer communications Portland: ACM Press 2004
21. Karev GP Wolf YI Rzhetsky AY Berezovskaya FS Koonin EV Birth and death of protein domains: A simple model of evolution explains power law behavior BMC Evol Biol 2002, 2:18 137606 12379152 10.1186/1471-2148-2-18
22. Koonin EV Wolf YI Karev GP The structure of the protein universe and genome evolution Nature 2002, 420:218-223 10.1038/nature01256 12432406
23. Lynch M The evolution of genetic networks by non-adaptive processes Nat Rev Genet 2007, 8:803-813 10.1038/nrg2192 17878896
24. Yip KY Yu H Kim PM Schultz M Gerstein M The tYNA platform for comparative interactomics: A web tool for managing, comparing and mining multiple networks Bioinformatics 2006, 22:2968-2970 10.1093/ bioinformatics/btl488 17021160