ArticleBMC bioinformatics2005
Alternative splicing and protein function.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
25 citing papers in PubMed, 47 citations in OpenAlex.
- Article
- Integrated top-down and bottom-up proteomics mass spectrometry for the characterization of endogenous ribosomal protein heterogeneity.Journal of pharmaceutical analysis · 2023Article
- Alternative splicing dynamics and evolutionary divergence during embryogenesis in wheat species.Plant biotechnology journal · 2021Article
- Direct Nanopore Sequencing of mRNA Reveals Landscape of Transcript Isoforms in Apicomplexan Parasites.mSystems · 2021Article
- Development and validation of an individual alternative splicing prognostic signature in gastric cancer.Aging · 2021Article
- Systematic profiling of alternative splicing inCancer cell international · 2020Article
- Alternative Splicing and Protein Diversity: Plants Versus Animals.Frontiers in plant science · 2019Review
- Alternative splicing and the evolution of phenotypic novelty.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Review
- A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling.Briefings in bioinformatics · 2016Article
- Coupling and coordination in gene expression processes with pre-mRNA splicing.International journal of molecular sciences · 2015Review
- Evolution of a potential hormone antagonist following gene splicing during primate evolution.PloS one · 2013Article
- Detecting splicing variants in idiopathic pulmonary fibrosis from non-differentially expressed genes.PloS one · 2013Article
- Projection of gene-protein networks to the functional space of the proteome and its application to analysis of organism complexity.BMC genomics · 2010Article
- Stochastic noise in splicing machinery.Nucleic acids research · 2009Article
- Splice-mediated Variants of Proteins (SpliVaP) - data and characterization of changes in signatures among protein isoforms due to alternative splicing.BMC genomics · 2008Article
- Positive selection in alternatively spliced exons of human genes.American journal of human genetics · 2008Article
- A procedure for identifying homologous alternative splicing events.BMC bioinformatics · 2007Article
- Alarin is a vasoactive peptide.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: high-resolution annotation for microarrays.BMC bioinformatics · 2007Article
- The (in)dependence of alternative splicing and gene duplication.PLoS computational biology · 2007Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlternative splicing is a major mechanism of generating protein diversity in higher eukaryotes. Although at least half, and probably more, of mammalian genes are alternatively spliced, it was not clear, whether the frequency of alternative splicing is the same in different functional categories. The problem is obscured by uneven coverage of genes by ESTs and a large number of artifacts in the EST data.
resultsWe have developed a method that generates possible mRNA isoforms for human genes contained in the EDAS database, taking into account the effects of nonsense-mediated decay and translation initiation rules, and a procedure for offsetting the effects of uneven EST coverage. Then we computed the number of mRNA isoforms for genes from different functional categories. Genes encoding ribosomal proteins and genes in the category "Small GTPase-mediated signal transduction" tend to have fewer isoforms than the average, whereas the genes in the category "DNA replication and chromosome cycle" have more isoforms than the average. Genes encoding proteins involved in protein-protein interactions tend to be alternatively spliced more often than genes encoding non-interacting proteins, although there is no significant difference in the number of isoforms of alternatively spliced genes.
conclusionFiltering for functional isoforms satisfying biological constraints and accounting for uneven EST coverage allowed us to describe differences in alternative splicing of genes from different functional categories. The observations seem to be consistent with expectations based on current biological knowledge: less isoforms for ribosomal and signal transduction proteins, and more alternative splicing of interacting and cell cycle proteins.
Indexed as
Identifiers
What OpenQuestion holds
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.