ArticlePloS one2013
Transcriptome sequencing of gene expression in the brain of the HIV-1 transgenic rat.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
31 citing papers in PubMed, 1 synthesis or guideline pooled it, 45 citations in OpenAlex.
- P-value evaluation, variability index and biomarker categorization for adaptively weighted Fisher's meta-analysis method in omics applications.Bioinformatics (Oxford, England) · 2020Pooled it
- Beneficial and adverse effects of THC on cognition in the HIV-1 transgenic rat model: Importance of exploring task- and sex-dependent outcomes.Brain, behavior, and immunity · 2025Article
- Acute Administration of HIV-1 Tat Protein Drives Glutamatergic Alterations in a Rodent Model of HIV-Associated Neurocognitive Disorders.Molecular neurobiology · 2024Article
- Advancing the preclinical study of comorbid neuroHIV and substance use disorders: Current perspectives and future directions.Brain, behavior, and immunity · 2023Review
- Update on Central Nervous System Effects of HIV in Adolescents and Young Adults.Current HIV/AIDS reports · 2023Review
- A sparse negative binomial mixture model for clustering RNA-seq count data.Biostatistics (Oxford, England) · 2022Article
- Using IPA tools to characterize molecular pathways underlying the involvement of IRF7 in antiviral response to HIV.NeuroImmune pharmacology and therapeutics · 2022Article
- Independent and Combined Effects of Nicotine or Chronic Tobacco Smoking and HIV on the Brain: A Review of Preclinical and Clinical Studies.Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2020Review
- Involvement of Interferon Regulatory Factor 7 in Nicotine's Suppression of Antiviral Immune Responses.Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2019Article
- White matter loss and oligodendrocyte dysfunction in HIV: A consequence of the infection, the antiretroviral therapy or both?Brain research · 2019Review
- Opioid and chemokine regulation of cortical synaptodendritic damage in HIV-associated neurocognitive disorders.Brain research · 2019Review
- Age-Related Decrease in Tyrosine Hydroxylase Immunoreactivity in the Substantia Nigra and Region-Specific Changes in Microglia Morphology in HIV-1 Tg Rats.Neurotoxicity research · 2019Article
- RNASeqDesign: A framework for RNA-Seq genome-wide power calculation and study design issues.Journal of the Royal Statistical Society. Series C, Applied statistics · 2019Article
- BAYESIAN LATENT HIERARCHICAL MODEL FOR TRANSCRIPTOMIC META-ANALYSIS TO DETECT BIOMARKERS WITH CLUSTERED META-PATTERNS OF DIFFERENTIAL EXPRESSION SIGNALS.The annals of applied statistics · 2019Article
- Modulatory Effects of Nicotine on neuroHIV/neuroAIDS.Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2018Review
- Dysregulation of Neuronal Cholesterol Homeostasis upon Exposure to HIV-1 Tat and Cocaine Revealed by RNA-Sequencing.Scientific reports · 2018Article
- HIV-1 Proteins Influence Novelty-Seeking Behavior and Alter Region-Specific Transcriptional Responses to Chronic Nicotine Treatment in HIV-1Tg Rats.Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco · 2017Article
- Biomarker detection and categorization in ribonucleic acid sequencing meta-analysis using Bayesian hierarchical models.Journal of the Royal Statistical Society. Series C, Applied statistics · 2017Article
- Chronic Binge Alcohol Administration Dysregulates Hippocampal Genes Involved in Immunity and Neurogenesis in Simian Immunodeficiency Virus-Infected Macaques.Biomolecules · 2016Article
- Gene Expression Profiles of HIV/AIDS Patients with Qi-Yin Deficiency and Dampness-Heat Retention.Journal of alternative and complementary medicine (New York, N.Y.) · 2016Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
Abstract
The noninfectious HIV-1 transgenic (HIV-1Tg) rat was developed as a model of AIDs-related pathology and immune dysfunction by manipulation of a noninfectious HIV-1(gag-pol) virus with a deleted 3-kb SphI-MscI fragment containing the 3' -region of gag and the 5' region of pol into F344 rats. Our previous studies revealed significant behavioral differences between HIV-1Tg and F344 control rats in their performance in the Morris water maze and responses to psychostimulants. However, the molecular mechanisms underlying these behavioral differences remain largely unknown. The primary goal of this study was to identify differentially expressed genes and enriched pathways affected by the gag-pol-deleted HIV-1 genome. Using RNA deep sequencing, we sequenced RNA transcripts in the prefrontal cortex, hippocampus, and striatum of HIV-1Tg and F344 rats. A total of 72 RNA samples were analyzed (i.e., 12 animals per group × 2 strains × 3 brain regions). Following deep-sequencing analysis of 50-bp paired-end reads of RNA-Seq, we used Bowtie/Tophat/Cufflinks suites to align these reads into transcripts based on the Rn4 rat reference genome and to measure the relative abundance of each transcript. Statistical analyses on each brain region in the two strains revealed that immune response- and neurotransmission-related pathways were altered in the HIV-1Tg rats, with brain region differences. Other neuronal survival-related pathways, including those encoding myelin proteins, growth factors, and translation regulators, were altered in the HIV-1Tg rats in a brain region-dependent manner. This study is the first deep-sequencing analysis of RNA transcripts associated the HIV-1Tg rat. Considering the functions of the pathways and brain regions examined in this study, our findings of abnormal gene expression patterns in HIV-1Tg rats suggest mechanisms underlying the deficits in learning and memory and vulnerability to drug addiction and other psychiatric disorders observed in HIV-positive patients.
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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.