ArticleBMC genomics2008
Performance comparison of two microarray platforms to assess differential gene expression in human monocyte and macrophage cells.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 48 citations in OpenAlex.
- Trial
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- Serum amyloid P component is an essential element of resistance against Aspergillus fumigatus.Nature communications · 2021Article
- Working Towards a Blood-Derived Gene Expression Biomarker Specific for Alzheimer's Disease.Journal of Alzheimer's disease : JAD · 2020Article
- Atlas of RNA sequencing profiles for normal human tissues.Scientific data · 2019Article
- Shambhala: a platform-agnostic data harmonizer for gene expression data.BMC bioinformatics · 2019Article
- The Pathway To Establishing HIV Latency Is Critical to How Latency Is Maintained and Reversed.Journal of virology · 2018Article
- Monocyte alterations in rheumatoid arthritis are dominated by preterm release from bone marrow and prominent triggering in the joint.Annals of the rheumatic diseases · 2018Article
- Review and Meta-Analyses of TAAR1 Expression in the Immune System and Cancers.Frontiers in pharmacology · 2018Article
- A compendium of monocyte transcriptome datasets to foster biomedical knowledge discovery.F1000Research · 2016Article
- Selecting Reliable mRNA Expression Measurements Across Platforms Improves Downstream Analysis.Cancer informatics · 2016Article
- A curated compendium of monocyte transcriptome datasets of relevance to human monocyte immunobiology research.F1000Research · 2016Article
- Article
- Integrative analysis of methylome and transcriptome in human blood identifies extensive sex- and immune cell-specific differentially methylated regions.Epigenetics · 2015Article
- Evaluation of Different Normalization and Analysis Procedures for Illumina Gene Expression Microarray Data Involving Small Changes.Microarrays (Basel, Switzerland) · 2013Article
- Extralymphocytic flexible immune recognition: a new angle on inflammation and aging.Aging and disease · 2012Article
- Article
- Gene expression reveals overlap between normal aging and Alzheimer's disease genes.Neurobiology of aging · 2011Article
- SIGNATURE: a workbench for gene expression signature analysis.BMC bioinformatics · 2011Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn this study we assessed the respective ability of Affymetrix and Illumina microarray methodologies to answer a relevant biological question, namely the change in gene expression between resting monocytes and macrophages derived from these monocytes. Five RNA samples for each type of cell were hybridized to the two platforms in parallel. In addition, a reference list of differentially expressed genes (DEG) was generated from a larger number of hybridizations (mRNA from 86 individuals) using the RNG/MRC two-color platform.
resultsOur results show an important overlap of the Illumina and Affymetrix DEG lists. In addition, more than 70% of the genes in these lists were also present in the reference list. Overall the two platforms had very similar performance in terms of biological significance, evaluated by the presence in the DEG lists of an excess of genes belonging to Gene Ontology (GO) categories relevant for the biology of monocytes and macrophages. Our results support the conclusion of the MicroArray Quality Control (MAQC) project that the criteria used to constitute the DEG lists strongly influence the degree of concordance among platforms. However the importance of prioritizing genes by magnitude of effect (fold change) rather than statistical significance (p-value) to enhance cross-platform reproducibility recommended by the MAQC authors was not supported by our data.
conclusionFunctional analysis based on GO enrichment demonstrates that the 2 compared technologies delivered very similar results and identified most of the relevant GO categories enriched in the reference list.
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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.