title: Geographical, environmental and pathophysiological influences on the human blood transcriptome.
abstract: Gene expression variation provides a read-out of both genetic and environmental influences on gene activity. Geographical, genomic and sociogenomic studies have highlighted how life circumstances of an individual modify the expression of hundreds and in some cases thousands of genes in a co-ordinated manner. This review places such results in the context of a conserved set of 90 transcripts known as Blood Informative Transcripts (BIT) that capture the major conserved components of variation in the peripheral blood transcriptome. Pathophysiological states are also shown to associate with the perturbation of transcript abundance along the major axes. Discussion of false negative rates leads us to argue that simple significance thresholds provide a biased perspective on assessment of differential expression that may cloud the interpretation of studies with small sample sizes.
authors.affiliation: School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
authors.forename: Rubina
authors.initials: R
authors.lastname: Tabassum
authors.affiliation: School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
authors.forename: Artika
authors.initials: A
authors.lastname: Nath
authors.affiliation: School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
authors.forename: Marcela
authors.initials: M
authors.lastname: Preininger
authors.affiliation: School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
authors.forename: Greg
authors.initials: G
authors.lastname: Gibson
keywords: Axes of variation; differential expression; eQTL; geographical genomics; sociogenomics
references.citation: Hum Hered. 1989;39(5):276-81
references.pmid: 2613254
references.citation: PLoS Genet. 2012;8(4):e1002639
references.pmid: 22532805
references.citation: Immunity. 2008 Jul 18;29(1):150-64
references.pmid: 18631455
references.citation: PLoS Genet. 2011 Feb;7(2):e1001317
references.pmid: 21383966
references.citation: Front Genet. 2012 Nov 09;3:243
references.pmid: 23162571
references.citation: Nat Immunol. 2011 Jul 10;12(8):786-95
references.pmid: 21743478
references.citation: PLoS One. 2013;8(3):e57766
references.pmid: 23469233
references.citation: Genes Immun. 2006 Jun;7(4):298-309
references.pmid: 16691187
references.citation: Evolution. 2005 Jan;59(1):126-37
references.pmid: 15792233
references.citation: J Invest Dermatol. 2012 Feb;132(2):466-8
references.pmid: 21993563
references.citation: FASEB J. 2004 Mar;18(3):534-6
references.pmid: 14734643
references.citation: Science. 2002 Dec 20;298(5602):2381-5
references.pmid: 12493913
references.citation: PLoS One. 2011;6(9):e24315
references.pmid: 21915309
references.citation: BMC Bioinformatics. 2008 May 20;9:244
references.pmid: 18492285
references.citation: PLoS Genet. 2011 Feb 03;7(2):e1002003
references.pmid: 21304890
references.citation: Arthritis Rheum. 2006 Nov;54(11):3601-11
references.pmid: 17075805
references.citation: PLoS Genet. 2008 Apr 11;4(4):e1000052
references.pmid: 18404217
references.citation: Proc Natl Acad Sci U S A. 1991 Feb 1;88(3):839-43
references.pmid: 1992475
references.citation: Mol Biol Evol. 1999 Sep;16(9):1166-77
references.pmid: 10486972
references.citation: Nat Genet. 2007 Feb;39(2):226-31
references.pmid: 17206142
references.citation: PLoS Genet. 2008 Dec;4(12):e1000294
references.pmid: 19057673
references.citation: PLoS Genet. 2010 May 27;6(5):e1000971
references.pmid: 20523906
references.citation: PLoS Genet. 2012 Aug;8(8):e1002886
references.pmid: 22927824
references.citation: Curr Opin Lipidol. 2013 Feb;24(1):57-64
references.pmid: 23069987
references.citation: PLoS Biol. 2007 Jul;5(7):e171
references.pmid: 17579516
references.citation: Am J Hum Genet. 2007 Mar;80(3):502-9
references.pmid: 17273971
references.citation: Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9440-5
references.pmid: 12883005
references.citation: PLoS Genet. 2013 Jun;9(6):e1003566
references.pmid: 23785302
references.citation: Genome Res. 2002 Apr;12(4):602-12
references.pmid: 11932244
references.citation: Ann Hum Genet. 2012 Mar;76(2):142-58
references.pmid: 22188222
references.citation: PLoS Genet. 2013;9(3):e1003362
references.pmid: 23516379
references.citation: Genome Biol. 2007;8(9):R189
references.pmid: 17854483
references.citation: Mol Biol Evol. 2009 Mar;26(3):649-58
references.pmid: 19091723
references.citation: PLoS Comput Biol. 2010 Aug 26;6(8):null
references.pmid: 20865155
references.citation: BMC Bioinformatics. 2008 Dec 29;9:559
references.pmid: 19114008
references.citation: Nat Rev Genet. 2010 Feb;11(2):137-48
references.pmid: 20084086
references.citation: Nat Genet. 2003 Mar;33(3):422-5
references.pmid: 12567189
references.citation: J Mol Evol. 1991 Dec;33(6):543-55
references.pmid: 1685753
references.citation: Arthritis Res Ther. 2011 Jul 06;13(4):228
references.pmid: 21745419
references.citation: Nat Rev Rheumatol. 2011 Jun 07;7(7):416-26
references.pmid: 21647204
references.citation: Hepatology. 2012 Mar;55(3):666-75
references.pmid: 22030901
references.citation: Bioinformatics. 2007 Jan 1;23(1):44-9
references.pmid: 17092989
references.citation: Genome Res. 2012 Mar;22(3):456-66
references.pmid: 22183966
references.citation: Science. 2009 Sep 4;325(5945):1246-50
references.pmid: 19644074
references.citation: Nat Rev Genet. 2005 Aug;6(8):623-32
references.pmid: 16012528
references.citation: Proc Natl Acad Sci U S A. 1994 Dec 6;91(25):12288-92
references.pmid: 7991620
references.citation: Nat Genet. 2007 Jul;39(7):807-8; author reply 808-9
references.pmid: 17597765
references.citation: PLoS Genet. 2009 May;5(5):e1000479
references.pmid: 19424432
references.citation: Mol Ecol. 2006 Apr;15(5):1197-211
references.pmid: 16626448
references.citation: Cytokine. 2006 Aug;35(3-4):148-53
references.pmid: 17027280
references.citation: Am J Hum Genet. 2008 Mar;82(3):631-40
references.pmid: 18313023
references.citation: Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14716-21
references.pmid: 19617551
references.citation: Am J Hum Genet. 2000 Mar;66(3):979-88
references.pmid: 10712212
references.citation: Nat Rev Genet. 2009 Feb;10(2):134-40
references.pmid: 19119265
references.citation: Nat Rev Immunol. 2011 Aug 05;11(9):625-32
references.pmid: 21818124
references.citation: Genetics. 1997 Mar;145(3):787-805
references.pmid: 9055088
references.citation: Nat Genet. 2003 Mar;33 Suppl:245-54
references.pmid: 12610534
references.citation: Nat Genet. 2010 Jan;42(1):62-7
references.pmid: 19966804
references.citation: PLoS Genet. 2011 Jun;7(6):e1002127
references.pmid: 21698142
references.citation: Nat Rev Genet. 2008 Aug;9(8):575-81
references.pmid: 18574472