ArticleNature methods2010
Alternative expression analysis by RNA sequencing.
Article in Nature methods, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 163 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
163 citing papers in PubMed.
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- Selection of Ideal Reference Genes for Gene Expression Analysis in COVID-19 and Mucormycosis.Microbiology spectrum · 2022Article
- Time-course full profiling of circulating miRNAs in neurologically deceased organ donors: a proof of concept study to understand the onset of the cytokine storm.Epigenetics · 2022Observational
- Comprehensive and scalable quantification of splicing differences with MntJULiP.Genome biology · 2022Article
- Single-Cell RNA-Seq Analysis of Cells from Degenerating and Non-Degenerating Intervertebral Discs from the Same Individual Reveals New Biomarkers for Intervertebral Disc Degeneration.International journal of molecular sciences · 2022Article
- Differential gene expression associated with a floral scent polymorphism in the evening primrose Oenothera harringtonii (Onagraceae).BMC genomics · 2022Article
- RNA-Seq is not required to determine stable reference genes for qPCR normalization.PLoS computational biology · 2022Article
- Interspecies transcriptomics identify genes that underlie disproportionate foot growth in jerboas.Current biology : CB · 2022Article
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- Genome-wide analysis of Claviceps paspali: insights into the secretome of the main species causing ergot disease in Paspalum spp.BMC genomics · 2021Article
- Alternative RNA splicing in stem cells and cancer stem cells: Importance of transcript-based expression analysis.World journal of stem cells · 2021Review
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- Predicting Agents That Can Overcome 5-FU Resistance in Colorectal Cancers via Pharmacogenomic Analysis.Biomedicines · 2021Article
- Lamin A/C Is Dispensable to Mechanical Repression of Adipogenesis.International journal of molecular sciences · 2021Article
- Alternative splicing acts as an independent prognosticator in ovarian carcinoma.Scientific reports · 2021Article
- Article
103 more citing papers are in PubMed but not listed here.
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Authors and funding
26 authors.
Funding
Abstract
In alternative expression analysis by sequencing (ALEXA-seq), we developed a method to analyze massively parallel RNA sequence data to catalog transcripts and assess differential and alternative expression of known and predicted mRNA isoforms in cells and tissues. As proof of principle, we used the approach to compare fluorouracil-resistant and -nonresistant human colorectal cancer cell lines. We assessed the sensitivity and specificity of the approach by comparison to exon tiling and splicing microarrays and validated the results with reverse transcription-PCR, quantitative PCR and Sanger sequencing. We observed global disruption of splicing in fluorouracil-resistant cells characterized by expression of new mRNA isoforms resulting from exon skipping, alternative splice site usage and intron retention. Alternative expression annotation databases, source code, a data viewer and other resources to facilitate analysis are available at http://www.alexaplatform.org/alexa_seq/.
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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.