ArticleBMC bioinformatics2007
In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
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- Gene expression profiles identify key factors in inflammatory odontoblastic dental pulp stem cell differentiation via TNFα/C5L2.Frontiers in genetics · 2025Article
- RNA sequencing and its applications in cancer and rare diseases.Molecular biology reports · 2022Review
- Integrated Genomic and Bioinformatics Approaches to Identify Molecular Links between Endocrine Disruptors and Adverse Outcomes.International journal of environmental research and public health · 2022Review
- Analysis of Staphylococcus aureus Transcriptome in Pediatric Soft Tissue Abscesses and Comparison to Murine Infections.Infection and immunity · 2021Article
- Experimental Strategies to Explore Drug Action and Resistance in Kinetoplastid Parasites.Microorganisms · 2020Review
- Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements.Bioinformatics (Oxford, England) · 2019Article
- Transcriptome Analysis Based on RNA-Seq in Understanding Pathogenic Mechanisms of Diseases and the Immune System of Fish: A Comprehensive Review.International journal of molecular sciences · 2018Review
- Benchmarking of RNA-sequencing analysis workflows using whole-transcriptome RT-qPCR expression data.Scientific reports · 2017Article
- RECoN: Rice Environment Coexpression Network for Systems Level Analysis of Abiotic-Stress Response.Frontiers in plant science · 2017Article
- An integrative transcriptomics approach identifies miR-503 as a candidate master regulator of the estrogen response in MCF-7 breast cancer cells.RNA (New York, N.Y.) · 2016Article
- Transcriptomic Determinants of Scrapie Prion Propagation in Cultured Ovine Microglia.PloS one · 2016Article
- BSND and ATP6V1G3: Novel Immunohistochemical Markers for Chromophobe Renal Cell Carcinoma.Medicine · 2015Article
- RNA Sequencing and Analysis.Cold Spring Harbor protocols · 2015Article
- Dual RNA sequencing reveals the expression of unique transcriptomic signatures in lipopolysaccharide-induced BV-2 microglial cells.PloS one · 2015Article
- Arabidopsis ensemble reverse-engineered gene regulatory network discloses interconnected transcription factors in oxidative stress.The Plant cell · 2014Article
- Article
- CLCA2 as a novel immunohistochemical marker for differential diagnosis of squamous cell carcinoma from adenocarcinoma of the lung.Disease markers · 2014Article
- Predicting gene function from uncontrolled expression variation among individual wild-type Arabidopsis plants.The Plant cell · 2013Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMicroarray co-expression signatures are an important tool for studying gene function and relations between genes. In addition to genuine biological co-expression, correlated signals can result from technical deficiencies like hybridization of reporters with off-target transcripts. An approach that is able to distinguish these factors permits the detection of more biologically relevant co-expression signatures.
resultsWe demonstrate a positive relation between off-target reporter alignment strength and expression correlation in data from oligonucleotide genechips. Furthermore, we describe a method that allows the identification, from their expression data, of individual probe sets affected by off-target hybridization.
conclusionThe effects of off-target hybridization on expression correlation coefficients can be substantial, and can be alleviated by more accurate mapping between microarray reporters and the target transcriptome. We recommend attention to the mapping for any microarray analysis of gene expression patterns.
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