Systematic analysis of gene expression in human brains before and after death

Genome Biology

Volumn 6, Issue 13, 2005, Pages

  Franz, Henriette ^a   Ullmann, Claudia ^b   Becker, Albert ^b   Ryan, Margaret ^c   Bahn, Sabine ^c   Arendt, Thomas ^d   Simon, Matthias ^b   Pääbo, Svante ^a   Khaitovich, Philipp ^a  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

^b UNIVERSITY HOSPITAL BONN   (Germany)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d UNIVERSITY OF LEIPZIG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ADOLESCENT; ADULT; AGED; ARTICLE; AUTOPSY; BRAIN REGION; CONTROLLED STUDY; DEATH; FEMALE; GENE EXPRESSION PROFILING; GENE FUNCTION; HUMAN; HUMAN TISSUE; MALE; SAMPLE; ANALYSIS OF VARIANCE; BRAIN; BRAIN CORTEX; CHILD; GENE EXPRESSION REGULATION; HIPPOCAMPUS; METABOLISM; MIDDLE AGED;

ADOLESCENT; AGED; AGED, 80 AND OVER; ANALYSIS OF VARIANCE; AUTOPSY; BRAIN; CEREBRAL CORTEX; CHILD; DEATH; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HIPPOCAMPUS; HUMANS; MALE; MIDDLE AGED;

EID: 33745054085     PISSN: 1474760X     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2005-6-13-r112     Document Type: Article

References (30)

1. Marcotte ER, Srivastava LK, Quirion R: cDNA microarray and proteomic approaches in the study of brain diseases: focus on schizophrenia and Alzheimer's disease. Pharmacol Ther 2003, 100:63-74.
2. Preuss TM, Caceres M, Oldham MC, Geschwind DH: Human brain evolution: insights from microarrays. Nat Rev Genet 2004, 5:850-860.
3. Vijg J, Calder RB: Transcripts of aging. Trends Genet 2004, 20:221-224.
4. Gotz J, Streffer JR, David D, Schild A, Hoerndli F, Pennanen L, Kurosinski P, Chen F: Transgenic animal models of Alzheimer's disease and related disorders: histopathology, behavior and therapy. Mol Psychiatry 2004, 9:664-683.
5. Soutourina O, Cheval L, Doucet A: Global analysis of gene expression in mammalian kidney. Pflugers Arch 2005, 450:13-25.
6. Bahn S, Augood SJ, Ryan M, Standaert DG, Starkey M, Emson PC: Gene expression profiling in the post-mortem human brain - no cause for dismay. J Chem Neuroanat 2001, 22:79-94.
7. Li JZ, Vawter MP, Walsh DM, Tomita H, Evans SJ, Choudary PV, Lopez JF, Avelar A, Shokoohi V, Chung T, et al.: Systematic changes in gene expression in postmortem human brains associated with tissue pH and terminal medical conditions. Hum Mol Genet 2004. 13:609-616.
8. Tomita H, Vawter MP, Walsh DM, Evans SJ, Choudary PV, Li J, Overman KM, Atz ME, Myers RM, Jones EG, et al.: 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.
9. Hynd MR, Lewohl JM, Scott HL, Dodd PR: Biochemical and molecular studies using human autopsy brain tissue. J Neurochem 2003. 85:543-562.
10. Castensson A, Emilsson L, Preece P, Jazin EE: High-resolution quantification of specific mRNA levels in human brain autopsies and biopsies. Genome Res 2000, 10:1219-1229.
11. Lukasiuk K, Pitkanen A: Large-scale analysis of gene expression in epilepsy research: is synthesis already possible? Neurochem Res 2004, 29:1169-1178.
12. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29.
13. Ryan MM, Huffaker SJ, Webster MJ, Wayland M. Freeman T, Bahn S: Application and optimization of microarray technologies for human postmortem brain studies. Biol Psychiatry 2004, 55:329-336.
14. Li J, Gould TD, Yuan P, Manji HK, Chen G: Post-mortem interval effects on the phosphorylation of signaling proteins. Neuropsychopharmacology 2003, 28:1017-1025.
15. Siew LK, Love S, Dawbarn D, Wilcock GK, Allen SJ: Measurement of pre- and post-synaptic proteins in cerebral cortex: effects of post-mortem delay. J Neurosci Methods 2004, 139:153-159.
16. Zhai QH, Ruebel K, Thompson GB, Lloyd RV: Androgen receptor expression in C-cells and in medullary thyroid carcinoma. Endocr Pathol 2003, 14:159-165.
17. Evans SJ, Choudary PV, Vawter MP, Li J, Meador-Woodruff JH, Lopez JF, Burke SM, Thompson RC, Myers RM, Jones EG, et al.: DNA microarray analysis of functionally discrete human brain regions reveals divergent transcriptional profiles. Neurobiol Dis 2003, 14:240-250.
18. Khaitovich P, Muetzel B, She X, Lachmann M, Hellmann I, Dietzsch J, Steigele S, Do HH, Weiss G, Enard W, et al.: Regional patterns of gene expression in human and chimpanzee brains. Genome Res 2004, 14:1462-1473.
19. Raghavan A, Ogilvie RL, Reilly C, Abelson ML, Raghavan S, Vasdewani J, Krathwohl M, Bohjanen PR: Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes. Nucleic Acids Res 2002, 30:5529-5538.
20. Yang E, van Nimwegen E, Zavolan M, Rajewsky N, Schroeder M, Magnasco M, Darnell JE Jr: Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. Genome Res 2003, 13:1863-1872.
21. Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, Brown PO: Precision and functional specificity in mRNA decay. Proc Natl Acad Sci USA 2002, 99:5860-5865.
22. ArrayExpress Database [http://www.ebi.ac.uk/arrayexpress/]
23. Bolstad BM, Irizarry RA, Astrand M, Speed TP: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19:185-193.
24. Ihaka R, Gentleman R: R: A language for data analysis and graphics. J Comp Graph Stat 1996, 5:299-314.
25. Significance Analysis of Microarrays [http://www-stat.stanford.edu/~tibs/SAM/]
26. Affymetrix [http://www.affymetrix.com]
27. LocusLink [ftp://ftp.ncbi.nih.gov/refseq/LocusLink]
28. Gene Ontology [http://www.godatabase.org/dev/database/archive]
29. GenMapper [http://ducati.izbi.uni-leipzig.de:8080/GenMapper/]
30. Do HH, Rahm E: Flexible integration of molecular-biological annotation data: The GenMapper approach. In 9th International Conference on Extending Database Technology: 14-18 June 2004; Heroklion Volume 2992. Springer LNCS; Springer-Verlag GMBH Germany: 2004:811-822.