Predictive networks: A flexible, open source, web application for integration and analysis of human gene networks

Nucleic Acids Research

Volumn 40, Issue D1, 2012, Pages

  Haibe Kains, Benjamin ^a,b   Olsen, Catharina ^c   Djebbari, Amira ^d,e   Bontempi, Gianluca ^c   Correll, Mick ^a   Bouton, Christopher ^f   Quackenbush, John ^a,b  

^a DANA FARBER CANCER INSTITUTE   (United States)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^c Machine Learning Group   (Belgium)

^d PRINCESS MARGARET HOSPITAL   (Canada)

^e UNIVERSITY OF TORONTO   (Canada)

^f Entagen   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER INTERFACE; COMPUTER NETWORK; GENE INTERACTION; GENE MUTATION; GENETIC ANALYSIS; GENOMICS; HUMAN; INFORMATION PROCESSING; INTEGRATION; ONCOGENE; PHENOTYPE; PREDICTIVE NETWORK; PRIORITY JOURNAL; WEB BROWSER;

DATABASES, GENETIC; GENE REGULATORY NETWORKS; GENOMICS; HUMANS; INTERNET; PHENOTYPE; USER-COMPUTER INTERFACE;

EID: 84862197985     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1050     Document Type: Article

References (49)

1. Spellman,P.T., Sherlock,G., Zhang,M.Q., Iyer,V.R., Anders,K., Eisen,M.B., Brown,P.O., Botstein,D. and Futcher,B. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell., 9, 3273-3297. (Pubitemid 28551928)
2. Friedman,N. (2004) Inferring cellular networks using probabilistic graphical models. Science, 303, 799-805.
3. Meyer,P.E., Kontos,K., Lafitte,F. and Bontempi,G. (2007) Information-theoretic inference of large transcriptional regulatory networks. EURASIP J. Bioinform. Syst. Biol., 2007, doi:10.1155/2007/79879.
4. Margolin,A.A., Nemenman,I., Basso,K., Wiggins,C., Stolovitzky,G., Favera,R. and Califano,A. (2006) ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics, 7, S7.
5. Faith,J.J., Hayete,B., Thaden,J.T., Mogno,I., Wierzbowski,J., Cottarel,G., Kasif,S., Collins,J.J. and Gardner,T.S. (2007) Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol., 5, e8.
6. Markowetz,F. (2010) How to understand the cell by breaking it: network analysis of gene perturbation screens. PLoS Comput. Biol., 6, e1000655.
7. Friedman,N., Linial,M., Nachman,I. and Pe'er,D. (2000) Using Bayesian networks to analyze expression data. In RECOMB '00: Proceedings of the Fourth Annual International Conference on Computational Molecular Biology. ACM, New York, NY, pp. 127-135.
8. Meyer,P.E., Kontos,K. and Bontempi,G. (2007) Biological network inference using redundancy analysis. Bioinformatics Research and Development, Vol. 4414, Springer, Berlin/Heidelberg, pp. 16-27.
9. Djebbari,A. and Quackenbush,J. (2008) Seeded Bayesian networks: constructing genetic networks from microarray data. BMC Syst. Biol., 2, 57.
10. Aburatani,S., Goto,K., Saito,S., Fumoto,M., Imaizumi,A., Sugaya,N., Murakami,H., Sato,M., Toh,H. and Horimoto,K. (2004) ASIAN: a website for network inference. Bioinformatics, 20, 2853-2856. (Pubitemid 39530179)
11. Taylor,R.C., Shah,A., Treatman,C. and Blevins,M. (2006) SEBINI: software environment for biological network inference. Bioinformatics, 22, 2706-2708. (Pubitemid 44642617)
12. Haverty,P.M., Frith,M.C. and Weng,Z. (2004) CARRIE web service: automated transcriptional regulatory network inference and interactive analysis. Nucleic Acids Res., 32, W213-W216. (Pubitemid 38997332)
13. Yngvadottir,B., Macarthur,D.G., Jin,H. and Tyler-Smith,C. (2009) The promise and reality of personal genomics. Genome Biol., 10, 237.
14. Fernald,G.H., Capriotti,E., Daneshjou,R., Karczewski,K.J. and Altman,R.B. (2011) Bioinformatics challenges for personalized medicine. Bioinformatics, 27, 1741-1748.
15. Mostafavi,S., Ray,D., Warde-Farley,D., Grouios,C. and Morris,Q. (2008) GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biol., 9(Suppl. 1), S4.
16. Hoffmann,R. and Valencia,A. (2005) Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics, 21, ii252-ii258. (Pubitemid 41535458)
17. Ikin,A., Riveros,C., Moscato,P. and Mendes,A. (2010) The gene interaction miner: a new tool for data mining contextual information for protein-protein interaction analysis. Bioinformatics, 26, 283-284.
18. GeneGo, Inc. USA GeneGO MetaCore. http://www.genego.com/metacore.php (31 August 2011, date last accessed).
19. Ingenuity System, Inc. USA Ingenuity Pathway Analysis. http://www.ingenuity.com/ (31 August 2011, date last accessed).
20. Sintek,M. and Decker,S. (2002) TRIPLE-a query, inference, and transformation language for the semantic web. In International Semantic Web Conference (ISWC), http://triple.semanticweb. org/doc/iswc2002/abstract/ (10 November 2011, date last accessed).
21. Cerami,E.G., Gross,B.E., Demir,E., Rodchenkov,I., Babur,O., Anwar,N., Schultz,N., Bader,G.D. and Sander,C. (2010) Pathway commons, a web resource for biological pathway data. Nucleic Acids Res., 39, D685-D690.
22. Wu,G., Feng,X. and Stein,L. (2010) A human functional protein interaction network and its application to cancer data analysis. Genome Biol., 11, R53.
23. Allias-i LingPipe. http://alias-i.com/lingpipe (31 August 2011, date last accessed).
24. Lora,V. and Gault,M.S.K.J.D. (2002) Variations in Medical Subject Headings (MeSH) mapping: from the natural language of patron terms to the controlled vocabulary of mapped lists. J. Med. Libr. Assoc., 90, 173.
25. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwoght,S.S., Eppig,J.T. et al. (2000) Gene ontology: tool for the unfication of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29. (Pubitemid 30257031)
26. Himsolt,M. Graph Modelling Language. http://www.fim.unipassau. de/en/fim/faculty/chairs/theoretische-informatik/projects. html (31 August 2011, date last accessed).
27. Shannon,P., Markiel,A., Ozier,O., Baliga,N.S., Wang,J.T., Ramage,D., Amin,N., Schwikowski,B. and Ideker,T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504. (Pubitemid 37428274)
28. Smoot,M.E., Ono,K., Ruscheinski,J., Wang,P.-L. and Ideker,T. (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics, 27, 431-432.
29. Brown,K.R., Otasek,D., Ali,M., McGuffin,M.J., Xie,W., Devani,B., Toch,I.L.V. and Jurisica,I. (2009) NAViGaTOR: network analysis, visualization and graphing Toronto. Bioinformatics, 25, 3327-3329.
30. Chickering,D.M. (1996) Learning from data: artificial intelligence and statistics V. In: Fisher,D. and Lenz,H.-J. (eds), Learning from Data: Artificial Intelligence and Statistics V. Springer, NY pp. 121-130.
31. Hayete,B., Gardner,T.S. and Collins,J.J. (2007) Size matters: network inference tackles the genome scale. Mol. Syst. Biol., 3, 77.
32. Haibe-Kains,B., Olsen,C., Bontempi,G. and Quackenbush,J. (2011) Predictionet: Inference for Predictive Networks Designed for (but not limited to) Genomic Data, https://github.com/bhaibeka/predictionet.
33. Bolstad,B.M., Irizarry,R.A., Astrand,M. and Speed,T.P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19, 185-193. (Pubitemid 36181903)
34. McCall,M.N., Bolstad,B.M. and Irizarry,R.A. (2010) Frozen robust multiarray analysis (fRMA). Biostatistics, 11, 242-253.
35. Steel,R.G.D. and Torrie,J.H. (1960) Principles and procedures of statistics: with special reference to the biological sciences. McGraw-Hill, University of Michigan, p. 481.
36. Matthews,B.W. (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta, 405, 442-451.
37. SpringSource. (2011) Groovy. http://groovy.codehaus.org/(31 August 2011, date last accessed).
38. SpringSource. (2009) Grails. http://grails.org/ (31 August 2011, date last accessed).
39. Krzywinski,M., Kasaian,K., Morozova,O., Birol,I., Jones,S. and Marra,M. (2010) Linear layout for visualization of networks. Genome Inform, http://mkweb.bcgsc.ca/linnet (30 August 2011, date last accessed).
40. Howe,D., Costanzo,M., Fey,P., Gojobori,T., Hannick,L., Hide,W., Hill,D.P., Kania,R., Schaeffer,M., St Pierre,S. et al. (2008) Big data: the future of biocuration. Nature, 455, 47-50.
41. Bateman,A. (2010) Curators of the world unite: the International Society of Biocuration. Bioinformatics, 26, 991.
42. Fackenthal,J.D. and Olopade,O.I. (2007) Breast cancer risk associated with BRCA1 and BRCA2 in diverse populations. Nat. Rev. Cancer, 7, 937-948. (Pubitemid 350165853)
43. Loi,S.M., Haibe-Kains,B., Majjaj,S., Lallemand,F., Durbecq,V., Larsimont,D., Gonzalez-Angulo,A.M., Pusztai,L., Symmans,W.F., Bardelli,A. et al. (2010) PIK3CA mutations associated with gene signature of low mTORC1 signaling and better outcomes in estrogen receptor-positive breast cancer. Proc. Natl Acad. Sci. USA, 107, 10208-10213.
44. Culhane,A.C., Schwarzl,T., Sultana,R., Picard,K.C., Picard,S.C., Lu,T.H., Franklin,K.R., French,S.J., Papenhausen,G., Correll,M. et al. (2010) GeneSigDB-a curated database of gene expression signatures. Nucleic Acids Res., 38, D716-D725.
45. Loi,S.M., Haibe-Kains,B., Desmedt,C., Wirapati,P., Lallemand,F., Tutt,A.M., Gillet,C., Ellis,P., Ryder,K., Reid,J.F. et al. (2008) Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen. BMC Genomics, 9, 239.
46. Ding,C. and Peng,H. (2005) Minimum redundancy feature selection from microarray gene expression data. J. Bioinform. Comput. Biol., 3, 185-205. (Pubitemid 40561382)
47. McGill,W.J. (1954) Multivariate information transmission. Psychometrika, 9, 97-116.
48. Meyer,P.E. (2008) Information-theoretic variable selection and network inference from microarray data. Ph.D. Thesis. UniversitéLibre de Bruxelles.
49. Neapolitan,R.E. (2003) Learning Bayesian networks. Prentice Hall, Upper Saddle River, NJ.