ArticleBMC genomics2014
A robust estimation of exon expression to identify alternative spliced genes applied to human tissues and cancer samples.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers, 1 of them a synthesis that pooled it.
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Who cites it
8 citing papers in PubMed, 1 synthesis or guideline pooled it, 14 citations in OpenAlex.
- Genome-wide Association Study Identifies a Regulatory Variant of RGMA Associated With Opioid Dependence in European Americans.Biological psychiatry · 2018Pooled it
- AML with complex karyotype: extreme genomic complexity revealed by combined long-read sequencing and Hi-C technology.Blood advances · 2023Article
- Splicing factor deficits render hematopoietic stem and progenitor cells sensitive to STAT3 inhibition.Cell reports · 2022Article
- Prognostic characteristics of immune subtypes associated with acute myeloid leukemia and their identification in cell subsets based on single-cell sequencing analysis.Frontiers in cell and developmental biology · 2022Article
- Chromosomal neighbourhoods allow identification of organ specific changes in gene expression.PLoS computational biology · 2021Article
- Article
- Analysis ofOncotarget · 2017Article
- RASA: Robust Alternative Splicing Analysis for Human Transcriptome Arrays.Scientific reports · 2015Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAccurate analysis of whole-gene expression and individual-exon expression is essential to characterize different transcript isoforms and identify alternative splicing events in human genes. One of the omic technologies widely used in many studies on human samples are the exon-specific expression microarray platforms.
resultsSince there are not many validated comparative analyses to identify specific splicing events using data derived from these types of platforms, we have developed an algorithm (called ESLiM) to detect significant changes in exon use, and applied it to a reference dataset of 270 human genes that show alternative expression in different tissues. We compared the results with three other methodological approaches and provided the R source code to be applied elsewhere. The genes positively detected by these analyses also provide a verified subset of human genes that present tissue-regulated isoforms. Furthermore, we performed a validation analysis on human patient samples comparing two different subtypes of acute myeloid leukemia (AML) and we experimentally validated the splicing in several selected genes that showed exons with highly significant signal change.
conclusionsThe comparative analyses with other methods using a fair set of human genes that show alternative splicing and the validation on clinical samples demonstrate that the proposed novel algorithm is a reliable tool for detecting differential splicing in exon-level expression data.
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