ArticleJournal of neuroscience methods2007
Methodological considerations for gene expression profiling of human brain.
Article in Journal of neuroscience methods, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers, 3 of them syntheses that pooled it.
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Who cites it
60 citing papers in PubMed, 3 syntheses or guidelines pooled it, 116 citations in OpenAlex.
- Neurotransmission-related gene expression in the frontal pole is altered in subjects with bipolar disorder and schizophrenia.Translational psychiatry · 2023Pooled it
- Concordance analysis of microarray studies identifies representative gene expression changes in Parkinson's disease: a comparison of 33 human and animal studies.BMC neurology · 2017Pooled it
- Brain expression genome-wide association study (eGWAS) identifies human disease-associated variants.PLoS genetics · 2012Pooled it
- Convergent Lower Expression of Redox-Linked Stress-Adaptation and Synaptic-Plasticity Genes in Major Depressive Disorder Across Seven Postmortem dlPFC Cohorts.Antioxidants (Basel, Switzerland) · 2026Article
- The influence of tissue pH and RNA integrity number on gene expression of human postmortem brain.Frontiers in psychiatry · 2023Article
- A Sensitization-Free Dimethyl Fumarate Prodrug, Isosorbide Di-(Methyl Fumarate), Provides a Topical Treatment Candidate for Psoriasis.JID innovations : skin science from molecules to population health · 2021Article
- Agonal Factors Distort Gene-Expression Patterns in Human Postmortem Brains.Frontiers in neuroscience · 2021Article
- Pathology and Biobanking.Turk patoloji dergisi · 2020Review
- Identification of potential diagnostic biomarkers for Parkinson's disease.FEBS open bio · 2019Article
- The Effects of Surgical Antiseptics and Time Delays on RNA Isolated From Human and Rodent Peripheral Nerves.Frontiers in cellular neuroscience · 2019Article
- Mitochondrial Complex I Deficiency in Schizophrenia and Bipolar Disorder and Medication Influence.Molecular neuropsychiatry · 2018Article
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- Characterization of RNA isolated from eighteen different human tissues: results from a rapid human autopsy program.Cell and tissue banking · 2016Article
- SNAP-25a/b Isoform Levels in Human Brain Dorsolateral Prefrontal Cortex and Anterior Cingulate Cortex.Molecular neuropsychiatry · 2015Article
- Elevated Hippocampal Cholinergic Neurostimulating Peptide precursor protein (HCNP-pp) mRNA in the amygdala in major depression.Journal of psychiatric research · 2015Article
- NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases.Database : the journal of biological databases and curation · 2015Article
- The alternative splicing of the apolipoprotein E gene is unperturbed in the brains of Alzheimer's disease patients.Molecular biology reports · 2014Article
- Integrative RNA-seq and microarray data analysis reveals GC content and gene length biases in the psoriasis transcriptome.Physiological genomics · 2014Article
- Comorbidities, confounders, and the white matter transcriptome in chronic alcoholism.Alcoholism, clinical and experimental research · 2014Article
Corrections and comments
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Authors and funding
17 authors at 4 institutions in 1 country.
Funding
Abstract
Gene expression profiles of postmortem brain tissue represent important resources for understanding neuropsychiatric illnesses. The impact(s) of quality covariables on the analysis and results of gene expression studies are important questions. This paper addressed critical variables which might affect gene expression in two brain regions. Four broad groups of quality indicators in gene expression profiling studies (clinical, tissue, RNA, and microarray quality) were identified. These quality control indicators were significantly correlated, however one quality variable did not account for the total variance in microarray gene expression. The data showed that agonal factors and low pH correlated with decreased integrity of extracted RNA in two brain regions. These three parameters also modulated the significance of alterations in mitochondrial-related genes. The average F-ratio summaries across all transcripts showed that RNA degradation from the AffyRNAdeg program accounted for higher variation than all other quality factors. Taken together, these findings confirmed prior studies, which indicated that quality parameters including RNA integrity, agonal factors, and pH are related to differences in gene expression profiles in postmortem brain. Individual candidate genes can be evaluated with these quality parameters in post hoc analysis to help strengthen the relevance to psychiatric disorders. We find that clinical, tissue, RNA, and microarray quality are all useful variables for collection and consideration in study design, analysis, and interpretation of gene expression results in human postmortem studies.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.