ArticleBriefings in bioinformatics2012
Probe mapping across multiple microarray platforms.
Article in Briefings in bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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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.
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Who cites it
15 citing papers in PubMed.
- Transcriptome analysis of early pregnancy vitamin D status and spontaneous preterm birth.PloS one · 2020Trial
- Deep immunophenotyping reveals clinically distinct cellular states and ecosystems in large-scale colorectal cancer.Communications biology · 2023Article
- Overnight Corticosterone and Gene Expression in Mouse Hippocampus: Time Course during Resting Period.International journal of molecular sciences · 2023Article
- Blood Transcript Biomarkers Selected by Machine Learning Algorithm Classify Neurodegenerative Diseases including Alzheimer's Disease.Biomolecules · 2022Article
- Early-pregnancy transcriptome signatures of preeclampsia: from peripheral blood to placenta.Scientific reports · 2020Article
- Identification of lncRNA competitively regulated subpathways in myocardial infarction.Experimental and therapeutic medicine · 2019Article
- Crosstalk analysis of dysregulated pathways in preeclampsia.Experimental and therapeutic medicine · 2019Article
- Generating a robust prediction model for stage I lung adenocarcinoma recurrence after surgical resection.Oncotarget · 2017Article
- A Novel Method to Identify Differential Pathways in Hippocampus Alzheimer's Disease.Medical science monitor : international medical journal of experimental and clinical research · 2017Article
- Integrative Analysis of Gene Networks and Their Application to Lung Adenocarcinoma Studies.Cancer informatics · 2017Article
- Identifying CDKN3 Gene Expression as a Prognostic Biomarker in Lung Adenocarcinoma via Meta-analysis.Cancer informatics · 2015Article
- The Sweden Cancerome Analysis Network - Breast (SCAN-B) Initiative: a large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine.Genome medicine · 2015Article
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- Ensemble-based network aggregation improves the accuracy of gene network reconstruction.PloS one · 2014Article
- Article
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Authors and funding
7 authors.
Funding
Abstract
Access to gene expression data has become increasingly common in recent years; however, analysis has become more difficult as it is often desirable to integrate data from different platforms. Probe mapping across microarray platforms is the first and most crucial step for data integration. In this article, we systematically review and compare different approaches to map probes across seven platforms from different vendors: U95A, U133A and U133 Plus 2.0 from Affymetrix, Inc.; HT-12 v1, HT-12v2 and HT-12v3 from Illumina, Inc.; and 4112A from Agilent, Inc. We use a unique data set, which contains 56 lung cancer cell line samples-each of which has been measured by two different microarray platforms-to evaluate the consistency of expression measurement across platforms using different approaches. Based on the evaluation from the empirical data set, the BLAST alignment of the probe sequences to a recent revision of the Transcriptome generated better results than using annotations provided by Vendors or from Bioconductor's Annotate package. However, a combination of all three methods (deemed the 'Consensus Annotation') yielded the most consistent expression measurement across platforms. To facilitate data integration across microarray platforms for the research community, we develop a user-friendly web-based tool, an API and an R package to map data across different microarray platforms from Affymetrix, Illumina and Agilent. Information on all three can be found at http://qbrc.swmed.edu/software/probemapper/.
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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.