ArticleNucleic acids research2010
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 150 papers, 5 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
150 citing papers in PubMed, 5 syntheses or guidelines pooled it, 260 citations in OpenAlex.
- Novel loci for childhood body mass index and shared heritability with adult cardiometabolic traits.PLoS genetics · 2020Pooled it
- Polymorphism at 19q13.41 Predicts Breast Cancer Survival Specifically after Endocrine Therapy.Clinical cancer research : an official journal of the American Association for Cancer Research · 2015Pooled it
- Expression Quantitative Trait Loci Information Improves Predictive Modeling of Disease Relevance of Non-Coding Genetic Variation.PloS one · 2015Pooled it
- A genome-wide association study identifies LIPA as a susceptibility gene for coronary artery disease.Circulation. Cardiovascular genetics · 2011Pooled it
- Multiple loci are associated with white blood cell phenotypes.PLoS genetics · 2011Pooled it
- Assessment of early response biomarkers in relation to long-term survival in patients with HER2-negative breast cancer receiving neoadjuvant chemotherapy plus bevacizumab: Results from the Phase II PROMIX trial.International journal of cancer · 2018Trial
- Dissecting the genetics of the human transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci†.Human molecular genetics · 2015Trial
- Statin-induced anti-proliferative effects via cyclin D1 and p27 in a window-of-opportunity breast cancer trial.Journal of translational medicine · 2015Trial
- Mediation analysis demonstrates that trans-eQTLs are often explained by cis-mediation: a genome-wide analysis among 1,800 South Asians.PLoS genetics · 2014Trial
- Reannotation of Public Transcriptomic Data Identifies Candidate lncRNAs and Putative Regulatory Networks in Rhabdomyosarcoma.Biomedicines · 2026Article
- Article
- Deconstructing Intratumoral Heterogeneity through Multiomic and Multiscale Analysis of Serial Sections.Cancers · 2024Article
- Deconstructing intratumoral heterogeneity through multiomic and multiscale analysis of serial sections.bioRxiv : the preprint server for biology · 2024Article
- C/EBPB-dependent adaptation to palmitic acid promotes tumor formation in hormone receptor negative breast cancer.Nature communications · 2022Article
- Genomic profiling and network-level understanding uncover the potential genes and the pathways in hepatocellular carcinoma.Frontiers in genetics · 2022Article
- Identification of a Two-lncRNA Signature with Prognostic and Diagnostic Value for Hepatocellular Carcinoma.Journal of oncology · 2022Article
- Impact of medication on blood transcriptome reveals off-target regulations of beta-blockers.PloS one · 2022Observational
- Echinacea purpurea (L.) Moench treatment of monocytes promotes tonic interferon signaling, increased innate immunity gene expression and DNA repeat hypermethylated silencing of endogenous retroviral sequences.BMC complementary medicine and therapies · 2021Article
- Distinct mechanisms of resistance to fulvestrant treatment dictate level of ER independence and selective response to CDK inhibitors in metastatic breast cancer.Breast cancer research : BCR · 2021Article
- Identification of distinct transcriptome signatures of human adipose tissue from fifteen depots.European journal of human genetics : EJHG · 2020Article
90 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
Illumina BeadArrays are among the most popular and reliable platforms for gene expression profiling. However, little external scrutiny has been given to the design, selection and annotation of BeadArray probes, which is a fundamental issue in data quality and interpretation. Here we present a pipeline for the complete genomic and transcriptomic re-annotation of Illumina probe sequences, also applicable to other platforms, with its output available through a Web interface and incorporated into Bioconductor packages. We have identified several problems with the design of individual probes and we show the benefits of probe re-annotation on the analysis of BeadArray gene expression data sets. We discuss the importance of aspects such as probe coverage of individual transcripts, alternative messenger RNA splicing, single-nucleotide polymorphisms, repeat sequences, RNA degradation biases and probes targeting genomic regions with no known transcription. We conclude that many of the Illumina probes have unreliable original annotation and that our re-annotation allows analyses to focus on the good quality probes, which form the majority, and also to expand the scope of biological information that can be extracted.
Indexed as
Identifiers
What OpenQuestion holds
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.