title: Pathprinting: An integrative approach to understand the functional basis of disease.
abstract: New strategies to combat complex human disease require systems approaches to biology that integrate experiments from cell lines, primary tissues and model organisms. We have developed Pathprint, a functional approach that compares gene expression profiles in a set of pathways, networks and transcriptionally regulated targets. It can be applied universally to gene expression profiles across species. Integration of large-scale profiling methods and curation of the public repository overcomes platform, species and batch effects to yield a standard measure of functional distance between experiments. We show that pathprints combine mouse and human blood developmental lineage, and can be used to identify new prognostic indicators in acute myeloid leukemia. The code and resources are available at http://compbio.sph.harvard.edu/hidelab/pathprint.
authors.affiliation: Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA.
authors.forename: Gabriel M
authors.initials: GM
authors.lastname: Altschuler
authors.affiliation: Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA ; Bioinformatics Core, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA ; Harvard Stem Cell Institute, 1350 Massachusetts Ave, Cambridge, MA 02138.
authors.forename: Oliver
authors.initials: O
authors.lastname: Hofmann
authors.affiliation: Ontario Institute for Cancer Research, Department of Informatics and Bio-computing, MaRS Centre, South Tower, 101 College Street, Toronto, ON, M5G 0A3, Canada.
authors.forename: Irina
authors.initials: I
authors.lastname: Kalatskaya
authors.affiliation: Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Payne
authors.affiliation: Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA ; Bioinformatics Core, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA.
authors.forename: Shannan J
authors.initials: SJ
authors.lastname: Ho Sui
authors.affiliation: Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA.
authors.forename: Uma
authors.initials: U
authors.lastname: Saxena
authors.affiliation: Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA.
authors.forename: Andrei V
authors.initials: AV
authors.lastname: Krivtsov
authors.affiliation: Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA ; Harvard Stem Cell Institute, 1350 Massachusetts Ave, Cambridge, MA 02138.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Armstrong
authors.affiliation: Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA.
authors.forename: Tianxi
authors.initials: T
authors.lastname: Cai
authors.affiliation: Ontario Institute for Cancer Research, Department of Informatics and Bio-computing, MaRS Centre, South Tower, 101 College Street, Toronto, ON, M5G 0A3, Canada.
authors.forename: Lincoln
authors.initials: L
authors.lastname: Stein
authors.affiliation: Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA ; Bioinformatics Core, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA ; Harvard Stem Cell Institute, 1350 Massachusetts Ave, Cambridge, MA 02138.
authors.forename: Winston A
authors.initials: WA
authors.lastname: Hide
references.citation: PLoS Comput Biol. 2009 Jan;5(1):e1000262
references.pmid: 19148271
references.citation: BMC Syst Biol. 2012 Jun 13;6:65
references.pmid: 22694839
references.citation: Cancer Cell. 2010 Jan 19;17(1):98-110
references.pmid: 20129251
references.citation: PLoS Biol. 2008 Jul 22;6(7):e184
references.pmid: 18651794
references.citation: BMC Bioinformatics. 2007 Sep 27;8:364
references.pmid: 17900369
references.citation: Nat Rev Genet. 2012 Jul 18;13(8):518-9
references.pmid: 22805699
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D760-5
references.pmid: 17099226
references.citation: J Biol Chem. 2007 Jul 20;282(29):21551-60
references.pmid: 17525163
references.citation: Brief Funct Genomics. 2011 Sep;10(5):280-93
references.pmid: 21764832
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D984-91
references.pmid: 22121217
references.citation: Curr Drug Metab. 2012 Sep 1;13(7):952-67
references.pmid: 22591344
references.citation: Bioinformatics. 2007 Nov 15;23(22):3103-4
references.pmid: 17895274
references.citation: JAMA. 2010 Dec 22;304(24):2706-15
references.pmid: 21177505
references.citation: Nat Methods. 2007 Nov;4(11):879
references.pmid: 17971777
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D13-25
references.pmid: 22140104
references.citation: Genome Biol. 2010 Jan 12;11(1):R3
references.pmid: 20067622
references.citation: J Immunol. 2011 Mar 1;186(5):3047-57
references.pmid: 21307297
references.citation: PLoS Comput Biol. 2008 Nov;4(11):e1000217
references.pmid: 18989396
references.citation: Blood. 2008 Nov 15;112(10):4193-201
references.pmid: 18716133
references.citation: Blood. 2008 May 1;111(9):4797-808
references.pmid: 18270328
references.citation: Genes Chromosomes Cancer. 2008 Jan;47(1):8-20
references.pmid: 17910043
references.citation: Nat Genet. 2000 May;25(1):25-9
references.pmid: 10802651
references.citation: Blood. 2009 Jul 9;114(2):257-60
references.pmid: 19433856
references.citation: Nucleic Acids Res. 2010 Jan;38(Database issue):D355-60
references.pmid: 19880382
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D691-7
references.pmid: 21067998
references.citation: Nature. 2010 Jul 29;466(7306):632-6
references.pmid: 20639864
references.citation: Arterioscler Thromb Vasc Biol. 2012 Feb;32(2):216-22
references.pmid: 22258904
references.citation: Blood. 2009 Mar 26;113(13):3088-91
references.pmid: 19171880
references.citation: BMC Bioinformatics. 2010 Dec 21;11:603
references.pmid: 21172034
references.citation: Cell. 2011 Jan 21;144(2):296-309
references.pmid: 21241896
references.citation: Nat Genet. 2005 Jan;37(1):48-55
references.pmid: 15608639
references.citation: Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50
references.pmid: 16199517
references.citation: Cell Stem Cell. 2007 Nov;1(5):578-91
references.pmid: 18371395
references.citation: BMC Cancer. 2011 Jul 20;11:304
references.pmid: 21774828
references.citation: BMC Bioinformatics. 2011 May 04;12:133
references.pmid: 21542931
references.citation: Nature. 2006 Aug 17;442(7104):818-22
references.pmid: 16862118
references.citation: BMC Genomics. 2010 Oct 18;11:574
references.pmid: 20955544
references.citation: PLoS One. 2011 Apr 29;6(4):e18968
references.pmid: 21559491
references.citation: Science. 2009 Jul 24;325(5939):435-9
references.pmid: 19589965
references.citation: BMC Bioinformatics. 2009 Feb 03;10:47
references.pmid: 19192285
references.citation: PLoS One. 2012;7(7):e40321
references.pmid: 22815738
references.citation: PLoS Comput Biol. 2008 Mar 28;4(3):e1000043
references.pmid: 18369433
references.citation: Proc Natl Acad Sci U S A. 2010 Apr 13;107(15):6994-9
references.pmid: 20335537
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D987-90
references.pmid: 23193272
references.citation: Bioinformatics. 2010 Oct 1;26(19):2416-23
references.pmid: 20702396
references.citation: Genome Biol. 2010;11(5):R53
references.pmid: 20482850
references.citation: Proc Natl Acad Sci U S A. 2005 Sep 20;102(38):13544-9
references.pmid: 16174746
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D1011-5
references.pmid: 21177656
references.citation: Genome Med. 2012 Mar 29;4(3):28
references.pmid: 22458606
references.citation: BMC Genomics. 2009 Dec 03;10 Suppl 3:S15
references.pmid: 19958478
references.citation: BMC Bioinformatics. 2009 Oct 08;10 Suppl 11:S12
references.pmid: 19811677