A cross-laboratory comparison of expression profiling data from normal human postmortem brain

Neuroscience

Volumn 167, Issue 2, 2010, Pages 384-395

  Mistry, M ^a   Pavlidis, P ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

Age; Genomics; Meta analysis; PH; Postmortem brain; Schizophrenia

Indexed keywords

BRAIN DERIVED NEUROTROPHIC FACTOR RECEPTOR; CELL ADHESION MOLECULE; CELL PROTEIN; EPIDERMAL GROWTH FACTOR RECEPTOR 3; EXCITATORY AMINO ACID TRANSPORTER 2; GLUTAMATE DECARBOXYLASE 67; GROWTH FACTOR; GUANYLATE KINASE; NEU DIFFERENTIATION FACTOR; PROTEIN DLG; PROTEIN NRG2; PROTEIN OPCML; PROTEIN PLDN; RGS4 PROTEIN; UNCLASSIFIED DRUG;

AGE DISTRIBUTION; ARTICLE; BRAIN CORTEX; BRAIN REGION; CADAVER; COMPARATIVE STUDY; CONTROLLED STUDY; DOWN REGULATION; FEMALE; GENDER; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; HUMAN; HUMAN TISSUE; MALE; NEUROTRANSMISSION; PH; PRIORITY JOURNAL; REGULATORY MECHANISM; SCHIZOPHRENIA; UPREGULATION;

AGE FACTORS; BRAIN; FEMALE; GENE EXPRESSION PROFILING; GENOME-WIDE ASSOCIATION STUDY; HUMANS; HYDROGEN-ION CONCENTRATION; MALE; POSTMORTEM CHANGES;

EID: 77950863035     PISSN: 03064522     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.neuroscience.2010.01.016     Document Type: Article

References (57)

1. Arion D., Unger T., Lewis D.A., Levitt P., Mirnics K. Molecular evidence for increased expression of genes related to immune and chaperone function in the prefrontal cortex in schizophrenia. Biol Psychiatry 2007, 62:711-721.
2. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M., Rubin G.M., Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29.
3. Bartke A. Impact of reduced insulin-like growth factor-1/insulin signaling on aging in mammals: novel findings. Aging Cell 2008, 7:285-290.
4. Berchtold N.C., Cribbs D.H., Coleman P.D., Rogers J., Head E., Kim R., Beach T., Miller C., Troncoso J., Trojanowski J.Q., Zielke H.R., Cotman C.W. Gene expression changes in the course of normal brain aging are sexually dimorphic. Proc Natl Acad Sci U S A 2008, 105:15605-15610.
5. Borozan I., Chen L., Paeper B., Heathcote J.E., Edwards A.M., Katze M., Zhang Z., McGilvray I.D. MAID: an effect size based model for microarray data integration across laboratories and platforms. BMC Bioinformatics 2008, 9:305.
6. Cahan P., Rovegno F., Mooney D., Newman J.C., St Laurent G., McCaffrey T.A. Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization. Gene 2007, 401:12-18.
7. Canales R.D., Luo Y., Willey J.C., Austermiller B., Barbacioru C.C., Boysen C., Hunkapiller K., Jensen R.V., Knight C.R., Lee K.Y., Ma Y., Maqsodi B., Papallo A., Peters E.H., Poulter K., Ruppel P.L., Samaha R.R., Shi L., Yang W., Zhang L., Goodsaid F.M. Evaluation of DNA microarray results with quantitative gene expression platforms. Nat Biotechnol 2006, 24:1115-1122.
8. Cashion A.B., Smith M.J., Wise P.M. Glutamic acid decarboxylase 67 (GAD67) gene expression in discrete regions of the rostral preoptic area change during the oestrous cycle and with age. J Neuroendocrinol 2004, 16:711-716.
9. Chen-Plotkin A.S., Geser F., Plotkin J.B., Clark C.M., Kwong L.K., Yuan W., et al. Variations in the progranulin gene affect global gene expression in frontotemporal lobar degeneration. Hum Mol Genet 2008, 17:1349-1362.
10. Choi K.H., Elashoff M., Higgs B.W., Song J., Kim S., Sabunciyan S., Diglisic S., Yolken R.H., Knable M.B., Torrey E.F., Webster M.J. Putative psychosis genes in the prefrontal cortex: combined analysis of gene expression microarrays. BMC Psychiatry 2008, 8:87.
11. Colantuoni C., Hyde T.M., Mitkus S., Joseph A., Sartorius L., Aguirre C., Creswell J., Johnson E., Deep-Soboslay A., Herman M.M., Lipska B.K., Weinberger D.R., Kleinman J.E. Age-related changes in the expression of schizophrenia susceptibility genes in the human prefrontal cortex. Brain Struct Funct 2008, 213:255-271.
12. Corfas G., Roy K., Buxbaum J.D. Neuregulin 1-erbB signaling and the molecular/cellular basis of schizophrenia. Nat Neurosci 2004, 7:575-580.
13. de Magalhaes J.P., Curado J., Church G.M. Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics 2009, 25:875-881.
14. Dobbin K.K., Beer D.G., Meyerson M., Yeatman T.J., Gerald W.L., Jacobson J.W., Conley B., Buetow K.H., Heiskanen M., Simon R.M., Minna J.D., Girard L., Misek D.E., Taylor J.M., Hanash S., Naoki K., Hayes D.N., Ladd-Acosta C., Enkemann S.A., Viale A., Giordano T.J. Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays. Clin Cancer Res 2005, 11:565-572.
15. El Idrissi A. Taurine improves learning and retention in aged mice. Neurosci Lett 2008, 436:19-22.
16. Elashoff M., Higgs B.W., Yolken R.H., Knable M.B., Weis S., Webster M.J., Barci B.M., Torrey E.F. Meta-analysis of 12 genomic studies in bipolar disorder. J Mol Neurosci 2007, 31:221-243.
17. Ernst C., Sequeira A., Klempan T., Ernst N., Ffrench-Mullen J., Turecki G. Confirmation of region-specific patterns of gene expression in the human brain. Neurogenetics 2007, 8:219-224.
18. Erraji-Benchekroun L., Underwood M.D., Arango V., Galfalvy H., Pavlidis P., Smyrniotopoulos P., Mann J.J., Sibille E. Molecular aging in human prefrontal cortex is selective and continuous throughout adult life. Biol Psychiatry 2005, 57:549-558.
19. Falls D.L. Neuregulins: functions, forms, and signaling strategies. Exp Cell Res 2003, 284:14-30.
20. Fisher R.A. Combining independent tests of significance. Am Stat 1948, 2:30.
21. Galfalvy H.C., Erraji-Benchekroun L., Smyrniotopoulos P., Pavlidis P., Ellis S.P., Mann J.J., Sibille E., Arango V. Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction. BMC Bioinformatics 2003, 4:37.
22. Harrison P.J., Heath P.R., Eastwood S.L., Burnet P.W., McDonald B., Pearson R.C. The relative importance of premortem acidosis and postmortem interval for human brain gene expression studies: selective mRNA vulnerability and comparison with their encoded proteins. Neurosci Lett 1995, 200:151-154.
23. Hess A., Iyer H. Fisher's combined p-value for detecting differentially expressed genes using Affymetrix expression arrays. BMC Genomics 2007, 8:96.
24. Hodges A., Strand A.D., Aragaki A.K., Kuhn A., Sengstag T., Hughes G., et al. Regional and cellular gene expression changes in human Huntington's disease brain. Hum Mol Genet 2006, 15:965-977.
25. Hong M.G., Myers A.J., Magnusson P.K., Prince J.A. Transcriptome-wide assessment of human brain and lymphocyte senescence. PLoS ONE 2008, 3:e3024.
26. Irizarry R.A., Warren D., Spencer F., Kim I.F., Biswal S., Frank B.C., Gabrielson E., Garcia J.G., Geoghegan J., Germino G., Griffin C., Hilmer S.C., Hoffman E., Jedlicka A.E., Kawasaki E., Martinez-Murillo F., Morsberger L., Lee H., Petersen D., Quackenbush J., Scott A., Wilson M., Yang Y., Ye S.Q., Yu W. Multiple-laboratory comparison of microarray platforms. Nat Methods 2005, 2:345-350.
27. Iwamoto K., Bundo M., Kato T. Altered expression of mitochondria-related genes in postmortem brains of patients with bipolar disorder or schizophrenia, as revealed by large-scale DNA microarray analysis. Hum Mol Genet 2005, 14:241-253.
28. Jiang C.H., Tsien J.Z., Schultz P.G., Hu Y. The effects of aging on gene expression in the hypothalamus and cortex of mice. Proc Natl Acad Sci U S A 2001, 98:1930-1934.
29. Khaitovich P., Muetzel B., She X., Lachmann M., Hellmann I., Dietzsch J., Steigele S., Do H.H., Weiss G., Enard W., Heissig F., Arendt T., Nieselt-Struwe K., Eichler E.E., Paabo S. Regional patterns of gene expression in human and chimpanzee brains. Genome Res 2004, 14:1462-1473.
30. Lee H.K., Braynen W., Keshav K., Pavlidis P. ErmineJ: tool for functional analysis of gene expression data sets. BMC Bioinformatics 2005, 6:269.
31. Levitt P., Ebert P., Mirnics K., Nimgaonkar V.L., Lewis D.A. Making the case for a candidate vulnerability gene in schizophrenia: convergent evidence for regulator of G-protein signaling 4 (RGS4). Biol Psychiatry 2006, 60:534-537.
32. Li J.Z., Meng F., Tsavaler L., Evans S.J., Choudary P.V., Tomita H., Vawter M.P., Walsh D., Shokoohi V., Chung T., Bunney W.E., Jones E.G., Akil H., Watson S.J., Myers R.M. Sample matching by inferred agonal stress in gene expression analyses of the brain. BMC Genomics 2007, 8:336.
33. Li J.Z., Vawter M.P., Walsh D.M., Tomita H., Evans S.J., Choudary P.V., Lopez J.F., Avelar A., Shokoohi V., Chung T., Mesarwi O., Jones E.G., Watson S.J., Akil H., Bunney W.E., Myers R.M. Systematic changes in gene expression in postmortem human brains associated with tissue pH and terminal medical conditions. Hum Mol Genet 2004, 13:609-616.
34. Li Z., Su Z., Wen Z., Shi L., Chen T. Microarray platform consistency is revealed by biologically functional analysis of gene expression profiles. BMC Bioinformatics 2009, 10(Suppl 11):S12.
35. Lockstone H.E., Harris L.W., Swatton J.E., Wayland M.T., Holland A.J., Bahn S. Gene expression profiling in the adult Down syndrome brain. Genomics 2007, 90:647-660.
36. Loerch P.M., Lu T., Dakin K.A., Vann J.M., Isaacs A., Geula C., Wang J., Pan Y., Gabuzda D.H., Li C., Prolla T.A., Yankner B.A. Evolution of the aging brain transcriptome and synaptic regulation. PLoS ONE 2008, 3:e3329.
37. Lu T., Pan Y., Kao S.Y., Li C., Kohane I., Chan J., Yankner B.A. Gene regulation and DNA damage in the ageing human brain. Nature 2004, 429:883-891.
38. Mexal S., Berger R., Adams C.E., Ross R.G., Freedman R., Leonard S. Brain pH has a significant impact on human postmortem hippocampal gene expression profiles. Brain Res 2006, 1106:1-11.
39. Middleton F.A., Mirnics K., Pierri J.N., Lewis D.A., Levitt P. Gene expression profiling reveals alterations of specific metabolic pathways in schizophrenia. J Neurosci 2002, 22:2718-2729.
40. Mirnics K., Levitt P., Lewis D.A. Critical appraisal of DNA microarrays in psychiatric genomics. Biol Psychiatry 2006, 60:163-176.
41. Myers A.J., Gibbs J.R., Webster J.A., Rohrer K., Zhao A., Marlowe L., et al. A survey of genetic human cortical gene expression. Nat Genet 2007, 39:1494-1499.
42. Oh S, Tseng GC, Sibille E (in press) Reciprocal phylogenetic conservation of molecular aging in mouse and human brain. Neurobiol Aging.
43. Pedotti P., t Hoen P.A., Vreugdenhil E., Schenk G.J., Vossen R.H., Ariyurek Y., de Hollander M., Kuiper R., van Ommen G.J., den Dunnen J.T., Boer J.M., de Menezes R.X. Can subtle changes in gene expression be consistently detected with different microarray platforms?. BMC Genomics 2008, 9:124.
44. Petersen D., Chandramouli G.V., Geoghegan J., Hilburn J., Paarlberg J., Kim C.H., Munroe D., Gangi L., Han J., Puri R., Staudt L., Weinstein J., Barrett J.C., Green J., Kawasaki E.S. Three microarray platforms: an analysis of their concordance in profiling gene expression. BMC Genomics 2005, 6:63.
45. R: A language and environment for statistical computing 2005, RDevelopmentCoreTeam, R Foundation for Statistical Computing, Vienna, Austria.
46. Reinius B., Saetre P., Leonard J.A., Blekhman R., Merino-Martinez R., Gilad Y., Jazin E. An evolutionarily conserved sexual signature in the primate brain. PLoS Genet 2008, 4 e1000100.
47. Rhodes D.R., Barrette T.R., Rubin M.A., Ghosh D., Chinnaiyan A.M. Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res 2002, 62:4427-4433.
48. Rhodes D.R., Yu J., Shanker K., Deshpande N., Varambally R., Ghosh D., Barrette T., Pandey A., Chinnaiyan A.M. Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci U S A 2004, 101:9309-9314.
49. Roth R.B., Hevezi P., Lee J., Willhite D., Lechner S.M., Foster A.C., Zlotnik A. Gene expression analyses reveal molecular relationships among 20 regions of the human CNS. Neurogenetics 2006, 7:67-80.
50. Shi L., Reid L.H., Jones W.D., Shippy R., Warrington J.A., Baker S.C., Collins P.J., de Longueville F., Kawasaki E.S., Lee K.Y., Luo Y., Sun Y.A., Willey J.C., Setterquist R.A., Fischer G.M., Tong W., Dragan Y.P., Dix D.J., Frueh F.W., Goodsaid F.M., Herman D., Jensen R.V., Johnson C.D., Lobenhofer E.K., Puri R.K., Schrf U., Thierry-Mieg J., Wang C., Wilson M., Wolber P.K., Zhang L., Amur S., Bao W., Barbacioru C.C., Lucas A.B., Bertholet V., Boysen C., Bromley B., Brown D., Brunner A., Canales R., Cao X.M., Cebula T.A., Chen J.J., Cheng J., Chu T.M., Chudin E., Corson J., Corton J.C., Croner L.J., Davies C., Davison T.S., Delenstarr G., Deng X., Dorris D., Eklund A.C., Fan X.H., Fang H., Fulmer-Smentek S., Fuscoe J.C., Gallagher K., Ge W., Guo L., Guo X., Hager J., Haje P.K., Han J., Han T., Harbottle H.C., Harris S.C., Hatchwell E., Hauser C.A., Hester S., Hong H., Hurban P., Jackson S.A., Ji H., Knight C.R., Kuo W.P., LeClerc J.E., Levy S., Li Q.Z., Liu C., Liu Y., Lombardi M.J., Ma Y., Magnuson S.R., Maqsodi B., McDaniel T., Mei N., Myklebost O., Ning B., Novoradovskaya N., Orr M.S., Osborn T.W., Papallo A., Patterson T.A., Perkins R.G., Peters E.H., Peterson R., Philips K.L., Pine P.S., Pusztai L., Qian F., Ren H., Rosen M., Rosenzweig B.A., Samaha R.R., Schena M., Schroth G.P., Shchegrova S., Smith D.D., Staedtler F., Su Z., Sun H., Szallasi Z., Tezak Z., Thierry-Mieg D., Thompson K.L., Tikhonova I., Turpaz Y., Vallanat B., Van C., Walker S.J., Wang S.J., Wang Y., Wolfinger R., Wong A., Wu J., Xiao C., Xie Q., Xu J., Yang W., Zhang L., Zhong S., Zong Y., Slikker W. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006, 24:1151-1161.
51. Shippy R., Fulmer-Smentek S., Jensen R.V., Jones W.D., Wolber P.K., Johnson C.D., Pine P.S., Boysen C., Guo X., Chudin E., Sun Y.A., Willey J.C., Thierry-Mieg J., Thierry-Mieg D., Setterquist R.A., Wilson M., Lucas A.B., Novoradovskaya N., Papallo A., Turpaz Y., Baker S.C., Warrington J.A., Shi L., Herman D. Using RNA sample titrations to assess microarray platform performance and normalization techniques. Nat Biotechnol 2006, 24:1123-1131.
52. Siegmund K.D., Connor C.M., Campan M., Long T.I., Weisenberger D.J., Biniszkiewicz D., Jaenisch R., Laird P.W., Akbarian S. DNA methylation in the human cerebral cortex is dynamically regulated throughout the life span and involves differentiated neurons. PLoS ONE 2007, 2:e895.
53. Somel M., Franz H., Yan Z., Lorenc A., Guo S., Giger T., et al. Transcriptional neoteny in the human brain. Proc Natl Acad Sci U S A 2009, 106:5743-5748.
54. Storey J.D., Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 2003, 100:9440-9445.
55. Tomita H., Vawter M.P., Walsh D.M., Evans S.J., Choudary P.V., Li J., Overman K.M., Atz M.E., Myers R.M., Jones E.G., Watson S.J., Akil H., Bunney W.E. Effect of agonal and postmortem factors on gene expression profile: quality control in microarray analyses of postmortem human brain. Biol Psychiatry 2004, 55:346-352.
56. Vawter M.P., Crook J.M., Hyde T.M., Kleinman J.E., Weinberger D.R., Becker K.G., Freed W.J. Microarray analysis of gene expression in the prefrontal cortex in schizophrenia: a preliminary study. Schizophr Res 2002, 58:11-20.
57. Vawter M.P., Evans S., Choudary P., Tomita H., Meador-Woodruff J., Molnar M., Li J., Lopez J.F., Myers R., Cox D., Watson S.J., Akil H., Jones E.G., Bunney W.E. Gender-specific gene expression in post-mortem human brain: localization to sex chromosomes. Neuropsychopharmacology 2004, 29:373-384.