Rich-Club phenomenon in the interactome of P. falciparum - Artifact or signature of a parasitic life style?

PLoS ONE

Volumn 2, Issue 3, 2007, Pages

  Wuchty, Stefan ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HUB PROTEIN; PROTOZOAL PROTEIN; RICH CLUB PROTEIN; UNCLASSIFIED DRUG; CAENORHABDITIS ELEGANS PROTEIN; DROSOPHILA PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; ARTIFACT; CAENORHABDITIS ELEGANS; CONSERVATION GENETICS; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; GENE FUNCTION; HOST PARASITE INTERACTION; MALARIA; NONHUMAN; PHYLOGENETIC TREE; PLASMODIUM FALCIPARUM; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; QUALITY CONTROL; SACCHAROMYCES CEREVISIAE; SPECIES INVASION; ANIMAL; ANIMAL BEHAVIOR; CHEMISTRY; CLASSIFICATION; GENETICS; HUMAN; MALARIA FALCIPARUM; METABOLISM; NUCLEOTIDE SEQUENCE; PARASITOLOGY; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DATABASE;

CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; EUKARYOTA; PLASMODIUM (APICOMPLEXA); PLASMODIUM FALCIPARUM;

ANIMALS; BEHAVIOR, ANIMAL; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; CONSERVED SEQUENCE; DATABASES, PROTEIN; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; HUMANS; MALARIA, FALCIPARUM; PLASMODIUM FALCIPARUM; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTOZOAN PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 55349132059     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0000335     Document Type: Article

References (26)

1. LaCount D, Vignali M, Chettier R, Phansalkar A, Bell R, et al. (2005) A protein interaction network of the malaria parasite plasmodium falciparum. Nature 438: 103-107.
2. Jeong H, Mason S, Barabasi A-L, Oltvai Z (2001) Lethality and centrality in protein networks. Nature 411: 41-42.
3. Barabasi A-L, Oltvai Z (2004) Network biology: Understanding the cell's functional organization. Nat Rev Gen 4: 101-113.
4. Fraser H, Hirsh A, Steinmetz L, Scharfe C, Feldman M (2002) Evolutionary rate in the protein interaction network. Science 296: 750-752.
5. Wuchty S, Oltvai Z, Barabasi A-L (2003) Evolutionary conservation of motif constituents within the yeast protein interaction network. Nat Genet 35: 176-179.
6. Wuchty S (2004) Topology and evolution in yeast interaction networks. Genome Res 14: 1310-1314.
7. Suthram S, Sittler T, Ideker T (2006) The plasmodium protein network diverges from those of other eukaryotes. Nature 438: 108-112.
8. Han J, Bertin N, Hao T, Goldberg DS, Berriz G, et al. (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430: 88-93.
9. Colizza V, Flamini A, Serano M, Vespignani A (2006) Detecting rich-club ordering in complex networks. Nat Physics 2: 110-115.
10. Maslov S, Sneppen K (2002) Specificity and stability in topology of protein networks. Science 296: 910-913.
11. Xenarios I, Salwinski L, Duan X, Higney P, Kim SM, et al. (2002) DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucl Acids Res 30: 303-305.
12. Giot L, Bader J, Brouwer C, Chaudhuri A, Kuang B, et al. (2004) A protein interaction map of drosophila melanogaster. Science 302: 1727-1736.
13. Remm M, Storm C, Sonnhammer E (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 314: 1041-1052.
14. Aravind L, Iyer L, Wellems T, Miller L (2003) Plasmodium biology: Genomic gleanings. Cell 115: 771-785.
15. Marti M, Good R, Rug M, Knuepfer E, Cowman A (2004) Targeting malaria virulence and remodeling proteins to the host erythrocyte. Science 306: 1930-1934.
16. Hiller N, Bhattacharjee S, van Ooij C, Liolios K, Harrison T, et al. (2004) A host-targeting signal in virulence proteins reveals a secretome in malarial infection. Science 306: 1934-1937.
17. Sargeant T, Marti M, Caler E, Carlton J, Simpson K, et al. (2006) Lineagespecific expansion of proteins exported to erythrocytes in malaria parasites. Genome Biol 7: R12.
18. Shannon P, Markiel A, Ozier O, Baliga N, Wang J, et al. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504.
19. Bozdech Z, Llinas M, Pulliam B, Wong E, Zhu J, et al. (2003) The transcriptome of the intraerythrocytic developmental cycle of plasmodium falciparum. PLoS Biology 1: 1-16.
20. Winzeler E (2006) Applied systems biology and malaria. Nat Rev Micro 4: 145-151.
21. Johnson KLJ, Florens L, Zhou Y, Santrosyan A, Grainger M, et al. (2004) Global analysis of transcript and protein levels across the plasmodium falciparum life cycle. Genome Res 14: 2308-2318.
22. Bahl A, Brunk B, Crabtree J, Fraunholz M, Gajria B, et al. (2003) Plasmodb: the plasmodium genome resource. a database integrating experimental and computational data. Nucl Acids Res 31: 212-215.
23. Han J, Dupuy D, Bertin N, Cusick M, Vidal M (2005) Effect of sampling on topology predictions of protein-protein interaction networks. Nat Biotech 23: 839-844.
24. Stumpf M, Wiuf C, May R (2005) Subnets of scale-free networks are not scalefree: Sampling properties of networks. Proc Natl Acad Sci USA 101: 4221-4224.
25. Von Mering C, Krause R, Snel B, Cornell M, Oliver S, et al. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417: 399-403.
26. Wuchty S, Barabasi A-L, Ferdig M (2006) Stable evolutionary signal in a protein interaction network of S. cerevisiae. BMC Evol Biol 6: 8.