Statistical Assessment of Crosstalk Enrichment between Gene Groups in Biological Networks

PLoS ONE

Volumn 8, Issue 1, 2013, Pages

  McCormack, Theodore ^a,b   Frings, Oliver ^a,b   Alexeyenko, Andrey ^a,c   Sonnhammer, Erik L L ^a,b,d  

^a SCIENCE FOR LIFE LABORATORY   (Sweden)

^b STOCKHOLM UNIVERSITY   (Sweden)

^c ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^d Linköping University   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ARTICLE; COMPUTER ANALYSIS; COMPUTER PROGRAM; GENE ENRICHMENT ANALYSIS; GENE IDENTIFICATION; GENETIC ALGORITHM; GENETIC DATABASE; GENETIC SCREENING; INTERMETHOD COMPARISON; LINK ASSIGMENT ALGORITHM; LINK ASSIGMENT+SECOND-ORDER ALGORITHM; LINK PERMUTATION ALGORITHM; MOLECULAR BIOLOGY; NODE PERMUTATION ALGORITHM; RELIABILITY; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE; STATISTICS;

COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; HUMANS; MODELS, STATISTICAL; REPRODUCIBILITY OF RESULTS; SIGNAL TRANSDUCTION; SOFTWARE;

EID: 84872806763     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0054945     Document Type: Article

References (36)

1. Deng M, Sun F, Chen T (2003) Assessment of the reliability of protein-protein interactions and protein function prediction. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing: 140-151.
2. Song J, Singh M, (2009) How and when should interactome-derived clusters be used to predict functional modules and protein function? Bioinformatics (Oxford, England) 25: 3143-3150.
3. Ostlund G, Lindskog M, Sonnhammer ELL, (2010) Network-based Identification of novel cancer genes. Molecular & cellular proteomics?: MCP 9: 648-655.
4. Hong M-G, Alexeyenko A, Lambert J-C, Amouyel P, Prince JA, (2010) Genome-wide pathway analysis implicates intracellular transmembrane protein transport in Alzheimer disease. Journal of human genetics 55: 707-709.
5. Storey JD, Tibshirani R, (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100: 9440-9445.
6. Ioannidis JPA, (2005) Why most published research findings are false. PLoS medicine 2: e124.
7. Milenković T, Filippis I, Lappe M, Przulj N, (2009) Optimized null model for protein structure networks. PloS One 4: e5967.
8. Erdös P, Rényi A, (1959) On random graphs, I. Publicationes Mathematicae (Debrecen). 6: 290-297.
9. Penrose M (2003) Random Geometric Graphs (Oxford Studies in Probability). {Oxford University Press, USA}.
10. Barabasi A, Albert R, (1999) Emergence of scaling in random networks. Science (New York, NY) 286: 509-512.
11. Alexeyenko A, Wassenberg DM, Lobenhofer EK, Yen J, Linney E, et al. (2010) Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicity. PloS One 5: e10465.
12. Li Y, Agarwal P, Rajagopalan D, (2008) A global pathway crosstalk network. Bioinformatics (Oxford, England) 24: 1442-1447.
13. Huttenhower C, Haley EM, Hibbs MA, Dumeaux V, Barrett DR, et al. (2009) Exploring the human genome with functional maps. Genome research 19: 1093-1106.
14. Maslov S, Sneppen K, (2002) Specificity and stability in topology of protein networks. Science (New York, NY) 296: 910-913.
15. Milo R, Kashtan N, Itzkovitz S, Newman M, Alon U (2004) On the uniform generation of random graphs with prescribed degree sequences. arXiv:cond-mat/0312028v2.
16. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, et al. (2002) Network motifs: simple building blocks of complex networks. Science (New York, NY) 298: 824-827.
17. Kuchaiev O, Rasajski M, Higham DJ, Przulj N, (2009) Geometric de-noising of protein-protein interaction networks. PLoS computational biology 5: e1000454.
18. Alexeyenko A, Sonnhammer ELL, (2009) Global networks of functional coupling in eukaryotes from comprehensive data integration. Genome research 19: 1107-1116.
19. Reynolds CA, Hong M-G, Eriksson UK, Blennow K, Wiklund F, et al. (2010) Analysis of lipid pathway genes indicates association of sequence variation near SREBF1/TOM1L2/ATPAF2 with dementia risk. Human molecular genetics 19: 2068-2078.
20. Newman MEJ, (2002) Assortative mixing in networks. Physical review letters 89: 208701.
21. Li L, Alderson D, Tanaka R, Doyle J, Willinger W (2005) Towards a Theory of Scale-Free Graphs: Definition, Properties, and Implications (Extended Version).
22. Annibale A, Coolen A, Fernandes L, Fraternali F, Kleinjung J (2009) Tailored graph ensembles as proxies or null models for real networks I: tools for quantifying structure. Journal of physics A: Mathematical and general 42.
23. Khatri P, Sirota M, Butte AJ, (2012) Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges. PLoS Comput Biol 8: e1002375.
24. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102: 15545-15550.
25. Abatangelo L, Maglietta R, Distaso A, D'Addabbo A, Creanza TM, et al. (2009) Comparative study of gene set enrichment methods. BMC bioinformatics 10: 275.
26. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics 25: 25-29.
27. Kanehisa M, Goto S, (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic acids research 28: 27-30.
28. Newman M (2003) The structure and function of complex networks. arXiv:cond-mat/0303516v1.
29. Benjamini Y, Hochberg Y, (1995) Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society 57: 289-300.
30. Taylor JR (1997) An introduction to error analysis: the study of uncertainties in physical measurements. University Science Books. p.
31. Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, et al. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic acids research 39: D561-8.
32. Huang DW, Sherman BT, Lempicki RA, (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic acids research 37: 1-13.
33. Setlur SR, Mertz KD, Hoshida Y, Demichelis F, Lupien M, et al. (2008) Estrogen-dependent signaling in a molecularly distinct subclass of aggressive prostate cancer. Journal of the National Cancer Institute 100: 815-825.
34. Moustakas A, Pardali K, Gaal A, Heldin C-H, (2002) Mechanisms of TGF-β signaling in regulation of cell growth and differentiation. Immunol Lett 82: 85-91.
35. Leong KG, Gao W-Q, (2008) The Notch pathway in prostate development and cancer. Differentiation; research in biological diversity 76: 699-716.
36. Lindgren D, Liedberg F, Andersson A, Chebil G, Gudjonsson S, et al. (2006) Molecular characterization of early-stage bladder carcinomas by expression profiles, FGFR3 mutation status, and loss of 9q. Oncogene 25: 2685-2696.