PAND: A distribution to identify functional linkage from networks with preferential attachment property

PLoS ONE

Volumn 10, Issue 7, 2015, Pages

  Li, Hua ^a,b   Tong, Pan ^b   Gallegos, Juan ^c   Dimmer, Emily ^d   Cai, Guoshuai ^b   Molldrem, Jeffrey J ^b   Liang, Shoudan ^a,b  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^c BAYLOR COLLEGE OF MEDICINE   (United States)

^d EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGICAL ACTIVITY; CONSTANTS AND COEFFICIENTS; EMPIRICAL CUMULATIVE DISTRIBUTION FUNCTION; HUMAN; MATHEMATICAL ANALYSIS; MONTE CARLO METHOD; NETWORK LEARNING; PREDICTION; PREFERENTIAL ATTACHMENT BASED COMMON NEIGHBOR DISTRIBUTION; PROBABILITY; PROTEIN CROSS LINKING; PROTEIN PROTEIN INTERACTION; RELIABILITY; SIMULATION; BIOLOGY; FACTUAL DATABASE; PROCEDURES;

COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; HUMANS; PROTEIN INTERACTION MAPS;

EID: 84941354445     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0127968     Document Type: Article

References (25)

1. Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, et al. PomBase: a comprehensive online resource for fission yeast. Nucleic Acids Res 2012, 40: D695-D699.
2. Vazquez A, Flammini A, Maritan A, Vespignani A. Global protein function prediction from protein-protein interaction networks. Nat Biotechnol 2003, 20: 697-700.
3. Barabasi A-L, Oltvai ZN. Network biology: understanding the cell's functional organization. Nature Rev Genet 2004, 5: 101-113.
4. Karaoz U, Murali TM, Letovsky S, Zheng Y, Ding C, Cantor CR, et al. Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci U S A 2004, 101: 2888-2893.
5. Rual J, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005, 437: 1173-1178.
6. Albert R. Network inference, analysis, and modeling in systems biology. Plant Cell 2007, 19: 3327-3338.
7. Sharan R, Ulitsky I, Shamir R. Network-based prediction of protein function. Mol Syst Bio 2007, 3:88.
8. Llewellyn R, Eisenberg DS. Annotating proteins with generalized functional linkages. Proc Natl Acad Sci U S A 2008, 105: 17700-17705.
9. Schwikowski B, Uetz P, Fields S. A network of protein-protein interactions in yeast. Nat Biotechnol 2000, 18: 1257-1261.
10. Hishigaki H, Nakai K, Ono T, Tanigami A, Takagi T. Assessment of prediction accuracy of protein function from protein-protein interaction data. Yeast 2001, 18: 523-531.
11. Samanta MP, Liang S. Predicting protein functions from redundancies in large-scale protein interaction networks. Proc Natl Acad Sci U S A 2003, 100: 12579-12583.
12. Brun C, Chevenet F, Martin D, Wojcik J, Guénoche A, Jacq B. Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network. Genome Biol 2003, 5: R6.
13. Letovsky S, Kasif S. Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics 2003, 19 Suppl. 1: i197-i204.
14. Chua HN, Sung WK, Wong L. Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions. Bioinformatics 2006, 22: 1623-1630.
15. Li H, Liang S. Local network topology in human protein interaction data predicts functional association. PLoS ONE 2009, 4(7): e6410.
16. Nabieva E, Jim K, Agarwal A, Chazelle B, Singh M. Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics 2005, 21: i302-i310.
17. Barabasi AL. Scale-free networks: a decade and beyond. Science 2009, 325: 412-413.
18. Barabasi AL, Albert R. Emergence of scaling in random networks. Science 1999, 286: 509-512.
19. Boccaletti S, Latora V, Moreno Y, Chavez M, Hwang D-U. Complex networks: structure and dynamics. Phys Rep 2006, 424: 175-308.
20. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. Nat Genet 2000, 25: 25-29.
21. Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 2000, 28: 27-30.
22. Erdos P, Renyi A. On random graphs. Publ Math (Debrecen) 1959, 6: 290.
23. Vidal M, Cusick ME, Barabasi AL. Interactome Networks and Human Disease. Cell 2011, 144: 986-998.
24. Kornberg RD. Mediator and the mechanism of transcriptional activation. Trends Biochem Sci 2005, 30 (5):235-239.
25. Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, van Berkum NL, et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 2010, 467(7314):430-435.