ArticlePloS one2015
Re-Annotator: Annotation Pipeline for Microarray Probe Sequences.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers, 5 of them syntheses that pooled it.
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Who cites it
59 citing papers in PubMed, 5 syntheses or guidelines pooled it.
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- Shared neuroimaging and molecular profiles in type 2 diabetes mellitus and major depressive disorder: an integrative analysis of genetic, transcriptomic, and neuroimaging data.Translational psychiatry · 2025Pooled it
- Gene co-expression changes underlying the functional connectomic alterations in Alzheimer's disease.BMC medical genomics · 2022Pooled it
- Differential and spatial expression meta-analysis of genes identified in genome-wide association studies of depression.Translational psychiatry · 2021Pooled it
- Genome-wide association studies of autoimmune vitiligo identify 23 new risk loci and highlight key pathways and regulatory variants.Nature genetics · 2016Pooled it
- Personalized prediction of treatment response during the acute phase of schizophrenia based on the connectome-based predictive model.European archives of psychiatry and clinical neuroscience · 2026Article
- Imaging patterns and genetic associations of brain atrophy across distinct symptom stages in Parkinson's disease.Neuroprotection (Chichester, England) · 2026Article
- Neuromodulation-induced normalization of cortical metastable dynamics signatures in Parkinson's disease.NPJ Parkinson's disease · 2026Article
- Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.iScience · 2026Article
- Transcriptional and neurotransmitter signatures associated with regional gray matter alterations in juvenile myoclonic epilepsy.Frontiers in molecular neuroscience · 2026Article
- Evidence for divergent cortical organisation in Parkinson's disease and Lewy Body Dementia.Nature communications · 2025Article
- Connectome-constrained ligand-receptor interaction analysis for understanding brain network communication.Nature communications · 2025Article
- Neural Plasticity Induced by Working Memory Training: Insights From Cortical Microstructure and Transcriptional Profiles.CNS neuroscience & therapeutics · 2025Article
- Substantial Heritability Underlies Fairness Norm Adaptation Capability and its Neural Basis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Differences in the amplitude of dynamic low-frequency fluctuations in primary angle-closure glaucoma are associated with gene-molecular multi-omics.Frontiers in medicine · 2025Article
- Transcriptional and neurotransmitter signatures of cerebral spontaneous neural activity in nurses with burnout.Frontiers in public health · 2025Article
- Article
- Molecular signatures of cortical expansion in the human foetal brain.Nature communications · 2024Article
- Molecular mechanisms underlying the neural correlates of working memory.BMC biology · 2024Article
- The genetics of spatiotemporal variation in cortical thickness in youth.Communications biology · 2024Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microarray technologies are established approaches for high throughput gene expression, methylation and genotyping analysis. An accurate mapping of the array probes is essential to generate reliable biological findings. However, manufacturers of the microarray platforms typically provide incomplete and outdated annotation tables, which often rely on older genome and transcriptome versions that differ substantially from up-to-date sequence databases. Here, we present the Re-Annotator, a re-annotation pipeline for microarray probe sequences. It is primarily designed for gene expression microarrays but can also be adapted to other types of microarrays. The Re-Annotator uses a custom-built mRNA reference database to identify the positions of gene expression array probe sequences. We applied Re-Annotator to the Illumina Human-HT12 v4 microarray platform and found that about one quarter (25%) of the probes differed from the manufacturer's annotation. In further computational experiments on experimental gene expression data, we compared Re-Annotator to another probe re-annotation tool, ReMOAT, and found that Re-Annotator provided an improved re-annotation of microarray probes. A thorough re-annotation of probe information is crucial to any microarray analysis. The Re-Annotator pipeline is freely available at http://sourceforge.net/projects/reannotator along with re-annotated files for Illumina microarrays HumanHT-12 v3/v4 and MouseRef-8 v2.
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