title: Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks.
abstract: Genomics provided us with an unprecedented quantity of data on the genes that are activated or repressed in a wide range of phenotypes. We have increasingly come to recognize that defining the networks and pathways underlying these phenotypes requires both the integration of multiple data types and the development of advanced computational methods to infer relationships between the genes and to estimate the predictive power of the networks through which they interact. To address these issues we have developed Predictive Networks (PN), a flexible, open-source, web-based application and data services framework that enables the integration, navigation, visualization and analysis of gene interaction networks. The primary goal of PN is to allow biomedical researchers to evaluate experimentally derived gene lists in the context of large-scale gene interaction networks. The PN analytical pipeline involves two key steps. The first is the collection of a comprehensive set of known gene interactions derived from a variety of publicly available sources. The second is to use these 'known' interactions together with gene expression data to infer robust gene networks. The PN web application is accessible from http://predictivenetworks.org. The PN code base is freely available at https://sourceforge.net/projects/predictivenets/.
authors.affiliation: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02215, USA, USA. bhaibeka@jimmy.harvard.edu
authors.forename: Benjamin
authors.initials: B
authors.lastname: Haibe-Kains
authors.forename: Catharina
authors.initials: C
authors.lastname: Olsen
authors.forename: Amira
authors.initials: A
authors.lastname: Djebbari
authors.forename: Gianluca
authors.initials: G
authors.lastname: Bontempi
authors.forename: Mick
authors.initials: M
authors.lastname: Correll
authors.forename: Christopher
authors.initials: C
authors.lastname: Bouton
authors.forename: John
authors.initials: J
authors.lastname: Quackenbush
mesh_terms: D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D023281:Genomics; D006801:Humans; D020407:Internet; D010641:Phenotype; D014584:User-Computer Interface
references.citation: Bioinformatics. 2011 Feb 1;27(3):431-2
references.pmid: 21149340
references.citation: Bioinformatics. 2010 Apr 15;26(8):991
references.pmid: 20305270
references.citation: Proc Natl Acad Sci U S A. 2010 Jun 1;107(22):10208-13
references.pmid: 20479250
references.citation: Nat Genet. 2000 May;25(1):25-9
references.pmid: 10802651
references.citation: Nature. 2008 Sep 4;455(7209):47-50
references.pmid: 18769432
references.citation: BMC Syst Biol. 2008 Jul 04;2:57
references.pmid: 18601736
references.citation: Mol Biol Cell. 1998 Dec;9(12):3273-97
references.pmid: 9843569
references.citation: Genome Biol. 2008;9 Suppl 1:S4
references.pmid: 18613948
references.citation: Biostatistics. 2010 Apr;11(2):242-53
references.pmid: 20097884
references.citation: EURASIP J Bioinform Syst Biol. 2007;:79879
references.pmid: 18354736
references.citation: PLoS Comput Biol. 2010 Feb 26;6(2):e1000655
references.pmid: 20195495
references.citation: Nat Rev Cancer. 2007 Dec;7(12):937-48
references.pmid: 18034184
references.citation: Bioinformatics. 2005 Sep 1;21 Suppl 2:ii252-8
references.pmid: 16204114
references.citation: BMC Bioinformatics. 2006 Mar 20;7 Suppl 1:S7
references.pmid: 16723010
references.citation: J Comput Biol. 2000;7(3-4):601-20
references.pmid: 11108481
references.citation: Mol Syst Biol. 2007;3:77
references.pmid: 17299414
references.citation: Biochim Biophys Acta. 1975 Oct 20;405(2):442-51
references.pmid: 1180967
references.citation: Bioinformatics. 2010 Jan 15;26(2):283-4
references.pmid: 19965878
references.citation: J Med Libr Assoc. 2002 Apr;90(2):173-80
references.pmid: 11999175
references.citation: BMC Genomics. 2008 May 22;9:239
references.pmid: 18498629
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D685-90
references.pmid: 21071392
references.citation: Genome Res. 2003 Nov;13(11):2498-504
references.pmid: 14597658
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D716-25
references.pmid: 19934259
references.citation: Bioinformatics. 2004 Nov 1;20(16):2853-6
references.pmid: 15130931
references.citation: Bioinformatics. 2009 Dec 15;25(24):3327-9
references.pmid: 19837718
references.citation: PLoS Biol. 2007 Jan;5(1):e8
references.pmid: 17214507
references.citation: Genome Biol. 2010;11(5):R53
references.pmid: 20482850
references.citation: J Bioinform Comput Biol. 2005 Apr;3(2):185-205
references.pmid: 15852500
references.citation: Bioinformatics. 2006 Nov 1;22(21):2706-8
references.pmid: 16954144
references.citation: Science. 2004 Feb 6;303(5659):799-805
references.pmid: 14764868
references.citation: Genome Biol. 2009;10(9):237
references.pmid: 19723346
references.citation: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W213-6
references.pmid: 15215383
references.citation: Bioinformatics. 2003 Jan 22;19(2):185-93
references.pmid: 12538238
references.citation: Bioinformatics. 2011 Jul 1;27(13):1741-8
references.pmid: 21596790