ArticleBMC genomics2009
Comprehensive splicing graph analysis of alternative splicing patterns in chicken, compared to human and mouse.
Article in BMC genomics, 2009. 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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Who cites it
15 citing papers in PubMed, 36 citations in OpenAlex.
- Functional analysis of theAnimal biotechnology · 2024Article
- Analysis of alternative splicing in chicken macrophages infected with avian pathogenicAnimal biotechnology · 2023Article
- RNA-seq Analysis Reveals Alternative Splicing Under Heat Stress in Rainbow Trout (Oncorhynchus mykiss).Marine biotechnology (New York, N.Y.) · 2022Article
- Genome-Wide Analysis of Alternative Splicing during Host-Virus Interactions in Chicken.Viruses · 2021Article
- Transcriptome-Wide Analyses Identify Dominant as the Predominantly Non-Conservative Alternative Splicing Inheritance Patterns in F1 Chickens.Frontiers in genetics · 2021Article
- Increased Alternative Splicing as a Host Response to Edwardsiella ictaluri Infection in Catfish.Marine biotechnology (New York, N.Y.) · 2018Article
- Deciphering alternative splicing and nonsense-mediated decay modulate expression in primary lymphoid tissues of birds infected with avian pathogenic E. coli (APEC).BMC genetics · 2017Article
- Correcting for differential transcript coverage reveals a strong relationship between alternative splicing and organism complexity.Molecular biology and evolution · 2014Article
- Article
- Pleiotropic and isoform-specific functions for Pitx2 in superior colliculus and hypothalamic neuronal development.Molecular and cellular neurosciences · 2013Article
- Exon-centric regulation of pyruvate kinase M alternative splicing via mutually exclusive exons.Journal of molecular cell biology · 2012Article
- Mutation of a U2 snRNA gene causes global disruption of alternative splicing and neurodegeneration.Cell · 2012Article
- The alternative splicing repressors hnRNP A1/A2 and PTB influence pyruvate kinase isoform expression and cell metabolism.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Genome-wide analysis of alternative splicing in cow: implications in bovine as a model for human diseases.BMC genomics · 2009Article
- High-throughput next-generation sequencing technologies foster new cutting-edge computing techniques in bioinformatics.BMC genomics · 2009Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlternative transcript diversity manifests itself as a prime cause of complexity in higher eukaryotes. Recently, transcript diversity studies have suggested that 60-80% of human genes are alternatively spliced. We have used a splicing pattern approach for the bioinformatics analysis of Alternative Splicing (AS) in chicken, human and mouse. Exons involved in splicing are subdivided into distinct and variant exons, based on the prevalence of the exons across the transcripts. Four possible permutations of these two different groups of exons were categorised as class I (distinct-variant), class II (distinct-variant), class III (variant-distinct) and class IV (variant-variant). This classification quantifies the variation in transcript diversity in the three species.
resultsIn all, 3901 chicken AS genes have been compared with 16,715 human and 16,491 mouse AS genes, with 23% of chicken genes being alternatively spliced, compared to 68% in humans and 57% in mice. To minimize any gene structure bias in the input data, comparative genome analysis has been carried out on the orthologous subset of AS genes for the three species. Gene-level analysis suggested that chicken genes show fewer AS events compared to human and mouse. An event-level analysis showed that the percentage of AS events in chicken is similar to that of human, which implies that a smaller number of chicken genes show greater transcript diversity. Overall, chicken genes were found to have fewer transcripts per gene and shorter introns than human and mouse genes.
conclusionIn chicken, the majority of genes generate only two or three isoforms, compared to almost eight in human and six in mouse. We observed that intron definition is expressed strongly when compared to exon definition for chicken genome, based on 3% intron retention in chicken, compared to 2% in human and mouse. Splicing patterns with variant exons account for 33% of AS chicken orthologous genes compared to 24% in human and 27% in mouse, providing a novel measure to describe the species-wise complexity due to alternative transcript diversity.
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