ReviewTrends in genetics : TIG2014
The emerging era of genomic data integration for analyzing splice isoform function.
Review in Trends in genetics : TIG, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 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.
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.
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Who cites it
44 citing papers in PubMed.
- Tissue-specific isoform usage and gene expression revealed through RNA-seq and ATAC-seq in developing cattle.BMC genomics · 2025Article
- Concordant Gene Expression and Alternative Splicing Regulation under Abiotic Stresses in Arabidopsis.Genes · 2024Article
- GeneFriends: gene co-expression databases and tools for humans and model organisms.Nucleic acids research · 2023Article
- Bridging the splicing gap in human genetics with long-read RNA sequencing: finding the protein isoform drivers of disease.Human molecular genetics · 2022Review
- Dominant transcript expression profiles of human protein-coding genes interrogated with GTEx dataset.Scientific reports · 2022Article
- Micro-dissection and integration of long and short reads to create a robust catalog of kidney compartment-specific isoforms.PLoS computational biology · 2022Article
- An integrated brain-specific network identifies genes associated with neuropathologic and clinical traits of Alzheimer's disease.Briefings in bioinformatics · 2022Article
- Integrative functional genomic analysis of intron retention in human and mouse brain with Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2021Article
- Differential Expression ofGenes · 2021Article
- Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells.Genome research · 2020Article
- Top-ranked expressed gene transcripts of human protein-coding genes investigated with GTEx dataset.Scientific reports · 2020Article
- Global quantitative analysis of the human brain proteome and phosphoproteome in Alzheimer's disease.Scientific data · 2020Article
- ClusterMine: A knowledge-integrated clustering approach based on expression profiles of gene sets.Journal of bioinformatics and computational biology · 2020Article
- A Literature Review of Gene Function Prediction by Modeling Gene Ontology.Frontiers in genetics · 2020Review
- Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources.Briefings in bioinformatics · 2019Review
- Tissue-specific mouse mRNA isoform networks.Scientific reports · 2019Article
- DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning.Bioinformatics (Oxford, England) · 2019Article
- Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometry.RSC advances · 2018Review
- Bioinformatics challenges and perspectives when studying the effect of epigenetic modifications on alternative splicing.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Review
- Exploiting differential RNA splicing patterns: a potential new group of therapeutic targets in cancer.Expert opinion on therapeutic targets · 2018Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
The vast majority of multi-exon genes in humans undergo alternative splicing, which greatly increases the functional diversity of protein species. Predicting functions at the isoform level is essential to further our understanding of developmental abnormalities and cancers, which frequently exhibit aberrant splicing and dysregulation of isoform expression. However, determination of isoform function is very difficult, and efforts to predict isoform function have been limited in the functional genomics field. Deep sequencing of RNA now provides an unprecedented amount of expression data at the transcript level. We describe here emerging computational approaches that integrate such large-scale whole-transcriptome sequencing (RNA-seq) data for predicting the functions of alternatively spliced isoforms, and we discuss their applications in developmental and cancer biology. We outline future directions for isoform function prediction, emphasizing the need for heterogeneous genomic data integration and tissue-specific, dynamic isoform-level network modeling, which will allow the field to realize its full potential.
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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.