ArticleBioinformatics (Oxford, England)2010
MADS+: discovery of differential splicing events from Affymetrix exon junction array data.
Article in Bioinformatics (Oxford, England), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
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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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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.
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Who cites it
27 citing papers in PubMed, 39 citations in OpenAlex.
- Alternative Splicing Regulation in Metabolic Disorders.Obesity reviews : an official journal of the International Association for the Study of Obesity · 2025Review
- Silencing proline-rich coiled-coil 2C inhibit the proliferation and metastasis of liver cancer cells.Journal of gastrointestinal oncology · 2023Article
- Overlapping Activities of Two Neuronal Splicing Factors Switch the GABA Effect from Excitatory to Inhibitory by Regulating REST.Cell reports · 2019Article
- Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm.BMC genomics · 2018Article
- Exon Array Biomarkers for the Differential Diagnosis of Schizophrenia and Bipolar Disorder.Molecular neuropsychiatry · 2018Article
- Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms.Briefings in bioinformatics · 2017Article
- EventPointer: an effective identification of alternative splicing events using junction arrays.BMC genomics · 2016Article
- Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions.Advances in experimental medicine and biology · 2016Article
- SNORD116 and SNORD115 change expression of multiple genes and modify each other's activity.Gene · 2015Article
- RASA: Robust Alternative Splicing Analysis for Human Transcriptome Arrays.Scientific reports · 2015Article
- Article
- Sudemycin E influences alternative splicing and changes chromatin modifications.Nucleic acids research · 2014Article
- Comprehensive analysis of alternative splicing in Digitalis purpurea by strand-specific RNA-Seq.PloS one · 2014Article
- Genome wide array analysis indicates that an amyotrophic lateral sclerosis mutation of FUS causes an early increase of CAMK2N2 in vitro.Biochimica et biophysica acta · 2013Article
- EGFR mutation-induced alternative splicing of Max contributes to growth of glycolytic tumors in brain cancer.Cell metabolism · 2013Article
- eQTL Mapping Using RNA-seq Data.Statistics in biosciences · 2013Article
- Pyrvinium pamoate changes alternative splicing of the serotonin receptor 2C by influencing its RNA structure.Nucleic acids research · 2013Article
- The RNA binding protein RBM38 (RNPC1) regulates splicing during late erythroid differentiation.PloS one · 2013Article
- Detecting splicing variants in idiopathic pulmonary fibrosis from non-differentially expressed genes.PloS one · 2013Article
- Valproic acid causes proteasomal degradation of DICER and influences miRNA expression.PloS one · 2013Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
motivationThe Affymetrix Human Exon Junction Array is a newly designed high-density exon-sensitive microarray for global analysis of alternative splicing. Contrary to the Affymetrix exon 1.0 array, which only contains four probes per exon and no probes for exon-exon junctions, this new junction array averages eight probes per probeset targeting all exons and exon-exon junctions observed in the human mRNA/EST transcripts, representing a significant increase in the probe density for alternative splicing events. Here, we present MADS+, a computational pipeline to detect differential splicing events from the Affymetrix exon junction array data. For each alternative splicing event, MADS+ evaluates the signals of probes targeting competing transcript isoforms to identify exons or splice sites with different levels of transcript inclusion between two sample groups. MADS+ is used routinely in our analysis of Affymetrix exon junction arrays and has a high accuracy in detecting differential splicing events. For example, in a study of the novel epithelial-specific splicing regulator ESRP1, MADS+ detects hundreds of exons whose inclusion levels are dependent on ESRP1, with a RT-PCR validation rate of 88.5% (153 validated out of 173 tested). AVAILABILITY: MADS+ scripts, documentations and annotation files are available at http://www.medicine.uiowa.edu/Labs/Xing/MADSplus/.
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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.