Estimating node degree in bait-prey graphs

Bioinformatics

Volumn 24, Issue 2, 2008, Pages 218-224

  Scholtens, Denise ^a   Chiang, Tony ^b   Huber, Wolfgang ^b   Gentleman, Robert ^c  

^a NORTHWESTERN UNIVERSITY   (United States)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c Fred Hutchinson Cancer Research Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROTEIN; INTERACTOME; UNCLASSIFIED DRUG;

ACCURACY; AMINO ACID SEQUENCE; ANALYTICAL ERROR; ARTICLE; CENTROMERE; CHROMOSOME; CONTROLLED STUDY; ENDOSOME; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; MATHEMATICAL COMPUTING; NONHUMAN; PRIORITY JOURNAL; PROBABILITY; PROTEIN ANALYSIS; PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE; STOCHASTIC MODEL;

ALGORITHMS; COMPUTER GRAPHICS; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; MODELS, BIOLOGICAL; MODELS, STATISTICAL; PROTEIN INTERACTION MAPPING; PROTEOME; SIGNAL TRANSDUCTION;

EID: 38349115657     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm565     Document Type: Article

References (16)

1. Barabási,A.-L. and Albert,R. (1999) Emergence of scaling in random networks. Science, 286, 509-512.
2. Chiang,T. et al. (2007) Coverage and error models of protein-protein interaction data by directed graph analysis. Genome Biol., 8, R186.
3. Collins,S. et al. (2007) Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol. Cell. Proteomics, 6, 439-450.
4. Deng,M. et al. (2003) Assessment of the reliability of protein-protein interactions and protein function prediction. Pac. Symp. Biocomput., 8, 140-151.
5. D'haeseleer,P. and Church,G. (2004) Estimating and improving protein interaction error rates. In Proceedings of the IEEE Computational Systems Bioinformatics Conference August 16-19 2004. IEEE Computer Society, California, pp. 216-223.
6. Gavin,A.C. et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415, 141-147.
7. Gavin,A.C. et al. (2006) Proteome survery reveals modularity of the yeast cell machinery. Nature, 440, 631-636.
8. Hart,G.T. et al. (2006) How complete are current yeast and human protein-interaction networks? Genome Biol., 7, 120.
9. Ho,Y. et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 415, 180-183.
10. Ito,T. et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA, 98, 4569-4574.
11. Krogan,N. et al. (2004) High-definition macromolecular composition of yeast RNA-processing complexes. Mol. Cell, 13, 225-239.
12. Krogan,N. et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature, 440, 637-643.
13. Li,L. et al. (2006) Towards a theory of scale-free graphs: Definition, properties, and implications. Internet Mathe., 2 4.
14. Mewes,H. et al. (2004) MIPS: Analysis and annotations of proteins from whole genomes. Nucleic Acids Res., 32, D41-D44.
15. The Gene Ontology Consortium (2000) Gene Ontology: Tool for the unification of biology. Nat. Genet., 25, 25-29.
16. Uetz,P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627.