Systematic evaluation of isoform function in literature reports of alternative splicing

Bhuiyan, Shamsuddin A.; Ly, Sophia; Phan, Minh; Huntington, Brandon; Hogan, Ellie; Cc, Liu; Liu, James H.; Pavlidis, Paul

doi:10.1101/303412

Cited by 2 publications

(2 citation statements)

References 49 publications

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“…promote apoptosis vs. cell proliferation, act as dominant negatives, etc.) [51][52][53]. Moreover, large-scale analyses of protein-protein interactions revealed that a large fraction of exon skipping events modulate interactions with specific partners, leading to the rewiring of interaction networks [54][55][56].…”

Section: 2) Exon Skipping-rich Transcriptomes In Bilateriansmentioning

confidence: 99%

Boosting Macroevolution: Genomic Changes Triggering Qualitative Expansions of Regulatory Potential

Irimia

Maeso

2019

Old Questions and Young Approaches to Animal Evolution

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Two main types of factors have been traditionally considered as potential driving forces underlying macroevolutionary patterns: environmental ('external') cues and genetic and/or developmental ('internal') factors. However, whereas the impact of non-gradual environmental changes has been extensively investigated, the contribution of internal causes, especially of genomic factors, has been approached in a less systematic manner, without clear definitions and classification schemes. Here, taking advantage of recent advances in comparative and functional genomics, we define three types of genomic changes that likely play important roles in macroevolutionary processes: (i) emergence of novel functional genomic properties, (ii) large-scale genome reshaping, and (iii) qualitative single amplifications of regulatory potentials (which we term quasa-regs). Their unifying theme is their ability to qualitatively expand the genomic regulatory potential of the species.We review examples in which these types of changes have likely played important roles and discuss their potential macroevolutionary implications. We conclude that, although such changes may have a minor organismal impact at the time of emergence, they are likely to often have profound long-term effects by expanding regulatory abilities and opening new highways that boost the evolutionary process.

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Section: 2) Exon Skipping-rich Transcriptomes In Bilateriansmentioning

confidence: 99%

Boosting Macroevolution: Genomic Changes Triggering Qualitative Expansions of Regulatory Potential

Irimia

Maeso

2019

Old Questions and Young Approaches to Animal Evolution

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“…For genes with multiple exons in the human genome, 95% are alternatively spliced [2] . AS is an important transcriptional regulation mechanism that increases the structural and functional diversity of gene products [3,4] . Several studies have found that AS is associated with cancers and other complex diseases [5][6][7][8] .…”

Section: Introductionmentioning

confidence: 99%

A comparison of computational approaches for intron retention detection

Zheng

Lin

et al. 2022

Big Data Min. Anal.

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Intron Retention (IR) is an alternative splicing mode through which introns are retained in mature RNAs rather than being spliced in most cases. IR has been gaining increasing attention in recent years because of its recognized association with gene expression regulation and complex diseases. Continuous efforts have been dedicated to the development of IR detection methods. These methods differ in their metrics to quantify retention propensity, performance to detect IR events, functional enrichment of detected IRs, and computational speed. A systematic experimental comparison would be valuable to the selection and use of existing methods. In this work, we conduct an experimental comparison of existing IR detection methods. Considering the unavailability of a gold standard dataset of intron retention, we compare the IR detection performance on simulation datasets. Then, we compare the IR detection results with real RNA-Seq data. We also describe the use of differential analysis methods to identify disease-associated IRs and compare differential IRs along with their Gene Ontology enrichment, which is illustrated on an Alzheimer's disease RNA-Seq dataset. We discuss key principles and features of existing approaches and outline their differences. This systematic analysis provides helpful guidance for interrogating transcriptomic data from the point of view of IR.

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Systematic evaluation of isoform function in literature reports of alternative splicing

Cited by 2 publications

References 49 publications

Boosting Macroevolution: Genomic Changes Triggering Qualitative Expansions of Regulatory Potential

Boosting Macroevolution: Genomic Changes Triggering Qualitative Expansions of Regulatory Potential

A comparison of computational approaches for intron retention detection

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