Cited by 331Molecular Biology Techniques and ApplicationsGene expression and cancer classificationSingle-cell and spatial transcriptomics

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Effect of agonal and postmortem factors on gene expression profile: quality control in microarray analyses of postmortem human brain

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Tomita, Hiroaki, Vawter, Marquis P, Walsh, David M, Evans, Simon J, Choudary, Prabhakara V, Li, Jun, Overman, Kevin M, Atz, Mary E, Myers, Richard M, Jones, Edward G, Watson, Stanley J, Akil, Huda, Bunney, William E·2004·Biological Psychiatry

DOI 10.1016/j.biopsych.2003.10.013PMC PMC3098566

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Abstract

There are major concerns that specific agonal conditions, including coma and hypoxia, might affect ribonucleic acid (RNA) integrity in postmortem brain studies. We report that agonal factors significantly affect RNA integrity and have a major impact on gene expression profiles in microarrays. In contrast to agonal factors, gender, age, and postmortem factors have less effect on gene expression profiles. The Average Correlation Index is proposed as a method for evaluating RNA integrity on the basis of similarity of microarray profiles. Reducing the variance due to agonal factors is critical in investigating small but validated gene expression differences in messenger RNA levels between psychiatric patients and control subjects.

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Authors: 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.
Affiliations: University of California, Irvine (US)
University of Michigan (US)
University of California, Davis (US)
Stanford University (US)
Corresponding author: Bunney, William E
ORCID: Tomita, Hiroaki
Vawter, Marquis P
Walsh, David M
Evans, Simon J
Choudary, Prabhakara V
Li, Jun
Myers, Richard M
Jones, Edward G
Watson, Stanley J
Akil, Huda
Bunney, William E
Venue: Biological Psychiatry
Publisher: Elsevier BV
Published: 2004-02
Volume: 55
Issue: 4
Pages: 346-352
ISSN: 0006-3223 (ISSN-L)
DOI: 10.1016/j.biopsych.2003.10.013
PMC: PMC3098566
OpenAlex: W2134441514
Cited by: 331
References: 38
Citations by year: 2026: 8 · 2025: 10 · 2024: 10 · 2023: 12 · 2022: 8 · 2021: 14 · 2020: 10 · 2019: 6 · 2018: 19 · 2017: 11 · 2016: 13 · 2015: 12 · 2014: 11 · 2013: 17 · 2012: 16
FWCI: 9.24
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Biological Psychiatry (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Funders: National Institute of Mental Health (P50MH60398, R01MH054844, MH54844, MH 42251, P50MH060398, P01MH042251)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Molecular Biology Techniques and Applications
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
Keywords: postmortem brain, gene expression profiles, RNA integrity, microarray quality control, hypoxia, coma, postmortem interval, psychiatric patients
MeSH terms: Adult, Aged, Autopsy, Brain Chemistry, Major Depressive Disorder, Humans, Male, Middle Aged, Postmortem Changes, Quality Control, RNA, Statistics as Topic, Time Factors, Reproducibility of Results, Gene Expression, Case-Control Studies, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling

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Effect of agonal and postmortem factors on gene expression profile: quality control in microarray analyses of postmortem human brain

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