Sex genes for genomic analysis in human brain: Internal controls for comparison of probe level data extraction

BMC Bioinformatics

Volumn 4, Issue , 2003, Pages

  Galfalvy, Hanga C ^a   Erraji Benchekroun, Loubna ^a,b   Smyrniotopoulos, Peggy ^a   Pavlidis, Paul ^b   Ellis, Steven P ^a,b   Mann, J John ^a,b   Sibille, Etienne ^a,b   Arango, Victoria ^a,b  

^a NEW YORK STATE PSYCHIATRIC INSTITUTE   (United States)

^b Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ACCURACY; ANALYTIC METHOD; ARTICLE; BRAIN REGION; CENTRAL NERVOUS SYSTEM; COMPUTER PROGRAM; CONTROLLED STUDY; DNA MICROARRAY; FEMALE; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC LINKAGE; HUMAN; HUMAN CELL; HUMAN TISSUE; INFORMATION PROCESSING; INTERMETHOD COMPARISON; MALE; NUCLEOTIDE SEQUENCE; PRACTICE GUIDELINE; PREFRONTAL CORTEX; QUALITY CONTROL; RELIABILITY; SEX CHROMOSOME; SEX DIFFERENCE; SIMULATION; STATISTICAL ANALYSIS; X CHROMOSOME; Y CHROMOSOME;

ANIMALIA;

EID: 2942516310     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-4-37     Document Type: Article

References (31)

1. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H and Brown EL: Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 1996, 14:1675-1680.
2. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B and Speed TP: Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003, 31:e15.
3. Xu J, Burgoyne PS and Arnold AP: Sex differences in sex chromosome gene expression in mouse brain. Hum Mol Genet 2002, 11:1409-1419.
4. Mayer A, Lahr G, Swaab DF, Pilgrim C and Reisert I: The Y-chromosomal genes SRY and ZFY are transcribed in adult human brain. Neurogenetics 1998, 1:281-288.
5. De Vries GJ, Rissman EF, Simerly RB, Yang LY, Scordalakes EM, Auger CJ, Swain A, Lovell-Badge R, Burgoyne PS and Arnold AP: A model system for study of sex chromosome effects on sexually dimorphic neural and behavioral traits. J Neurosci 2002, 22:9005-9014.
6. Luders E, Steinmetz H and Jancke L: Brain size and grey matter volume in the healthy human brain. Neuroreport 2002, 13:2371-2374.
7. Swaab DF and Hofman MA: Sexual differentiation of the human brain. A historical perspective. Prog Brain Res 1984, 61:361-374.
8. Swaab DF and Hofman MA: Sexual differentiation of the human hypothalamus in relation to gender and sexual orientation. Trends Neurosci 1995, 18:264-270.
9. Rabinowicz T, Petetot JM, Gartside PS, Sheyn D, Sheyn T and de CM: Structure of the cerebral cortex in men and women. J Neuropathol Exp Neurol 2002, 61:46-57.
10. Shaywitz BA, Shaywitz SE, Pugh KR, Constable RT, Skudlarski P, Fulbright RK, Bronen RA, Fletcher JM, Shankweiler DP and Katz L: Sex differences in the functional organization of the brain for language. Nature 1995, 373:607-609.
11. Tordjman S, Roubertoux PL, Carlier M, Moutier R, Anderson G, Launay M and Degrelle H: Linkage between brain serotonin concentration and the sex-specific part of the Y-chromosome in mice. Neurosci Lett 1995, 183:190-192.
12. Nishizawa S, Benkelfat C, Young SN, Leyton M, Mzengeza S, de Montigny C, Blier P and Diksic M: Differences between males and females in rates of serotonin synthesis in human brain. Proc Natl Acad Sci U S A 1997, 94:5308-5313.
13. Mann JJ, Huang YY, Underwood MD, Kassir SA, Oppenheim S, Kelly TM, Dwork AJ and Arango V: A serotonin transporter gene promoter polymorphism (5-HTTLPR) and prefrontal cortical binding in major depression and suicide. Arch Gen Psychiatry 2000, 57:729-738.
14. Guillot PV, Carlier M, Maxson SC and Roubertoux PL: Intermale aggression tested in two procedures, using four inbred strains of mice and their reciprocal congenics: Y chromosomal implications. Behav Genet 1995, 25:357-360.
15. Ratcliffe SG, Butler GE and Jones M: Edinburgh study of growth and development of children with sex chromosome abnormalities. IV. Birth Defects Orig Artic Ser 1990, 26:1-44.
16. Beyer C, Pilgrim C and Reisert I: Dopamine content and metabolism in mesencephalic and diencephalic cell cultures: sex differences and effects of sex steroids. J Neurosci 1991, 11:1325-1333.
17. Carruth LL, Reisert I and Arnold AP: Sex chromosome genes directly affect brain sexual differentiation. Nat Neurosci 2002, 5:933-934.
18. Li C and Wong WH: Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proc Natl Acad Sci U S A 2001, 98:31-36.
19. Reiner A, Yekutieli D and Benjamini Y: Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics 2003, 19:368-375.
20. Harrison PJ, Heath PR, Eastwood SL, Burnet PW, McDonald B and Pearson RC: 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.
21. Ellis SP, Underwood MD, Arango V and Mann JJ: Mixed models and multiple comparisons in analysis of human neurochemical maps. Psychiatry Res 2000, 99:111-119.
22. Efron B, Tibshirani R, Storey JD and Tusher V: Empirical Bayes analysis of a microarray experiment. Journal of the American Statistical Association 2001, 96:1151-1160.
23. Storey JD and Tibshirani R: Estimating False DiscoveryRates Under Dependence with Applications to DNA Microarrays. Technical report 2001 [http://www-stat.stanford.edu/~tibs/research.html].
24. Benjamini Y and Yekutieli D: The control of the false discovery rate in multiple testing under dependency. Annals of Statistics 2001, 29:1165-1188.
25. Johnston NL, Cervenak J, Shore AD, Torrey EF, Yolken RH and Cerevnak J: Multivariate analysis of RNA levels from postmortem human brains as measured by three different methods of RT-PCR. Stanley Neuropathology Consortium. J Neurosci Methods 1997, 77:83-92.
26. Mirnics K, Middleton FA, Marquez A, Lewis DA and Levitt P: Molecular characterization of schizophrenia viewed by microarray analysis of gene expression in prefrontal cortex. Neuron 2000, 28:53-67.
27. Willard HF: X chromosome inactivation, XIST, and pursuit of the X-inactivation center. Cell 1996, 86:5-7.
28. Lahn BT and Page DC: Functional coherence of the human Y chromosome. Science 1997, 278:675-680.
29. Arango V, Underwood MD, Gubbi AV and Mann JJ: Localized alterations in pre- and postsynaptic serotonin binding sites in the ventrolateral prefrontal cortex of suicide victims. Brain Res 1995, 688:121-133.
30. Mosteller F and Tukey JW: Data analysis and regression: A secondary course in statistics. Reading MA : Addison-Wesley Publishing Co. Inc; 1977.
31. Benjamini Y and Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, Series B, Methodological 1995, 57:289-300.