A bioinformatic survey of RNA isoform diversity and expression across 9 GTEx tissues using long-read sequencing data [PDF]
BMC GenomicsBackground Even though alternative RNA splicing was discovered nearly 50 years ago (1977), we still understand very little about most isoforms arising from a single gene, including in which tissues they are expressed and if their functions differ.
Madeline L. Page +7 more
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A ratiometric catalog of protein isoform shifts in the cardiac fetal gene program [PDF]
JCI InsightPathological cardiac remodeling is associated with the reactivation of fetal genes, yet the extent of the heart’s fetal gene program and its impact on proteome compositions remain incompletely understood.
Yu Han +6 more
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Dissecting the Biological Functions of Various Isoforms of Ferredoxin Reductase for Cell Survival and DNA Damage Response [PDF]
CellsThe ferredoxin reductase (FDXR) gene is expressed as seven isoforms: 1–6 by alternative splicing and 7 by an alternative promoter according to the Entrez Gene Database.
Ken-ichi Nakajima +4 more
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Integrating whole genome and transcriptome sequencing to characterize the genetic architecture of isoform variation [PDF]
Nature CommunicationsWe present a whole-blood isoform ratio QTL (irQTL) resource by analyzing genome-wide isoform-to-gene expression ratios using sequencing data. In Framingham Heart Study (FHS, n = 2622) discovery, we identify over 1.1 million cis-irQTLs (minor allele ...
Chunyu Liu +24 more
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Computational and Structural Biotechnology Journal, 2021 Transcript isoforms regulated by alternative splicing can substantially impact carcinogenesis, leading to a need to obtain clues for both gene differential expression and malfunctions of isoform distributions in cancer studies.
Tzu-Hsien Yang +8 more
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TAGET: a toolkit for analyzing full-length transcripts from long-read sequencing
Nature Communications, 2023 Single-molecule Real-time Isoform Sequencing (Iso-seq) of transcriptomes by PacBio can generate very long and accurate reads, thus providing an ideal platform for full-length transcriptome analysis.
Yuchao Xia +10 more
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Frontiers in Genetics, 2021 The SALL2 transcription factor, an evolutionarily conserved gene through vertebrates, is involved in normal development and neuronal differentiation. In disease, SALL2 is associated with eye, kidney, and brain disorders, but mainly is related to cancer ...
Carlos Farkas +9 more
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A large-scale comparative study of isoform expressions measured on four platforms
BMC Genomics, 2020 Background Most eukaryotic genes produce different transcripts of multiple isoforms by inclusion or exclusion of particular exons. The isoforms of a gene often play diverse functional roles, and thus it is necessary to accurately measure isoform ...
Wei Zhang +6 more
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Improved prediction of smoking status via isoform-aware RNA-seq deep learning models.
PLoS Computational Biology, 2021 Most predictive models based on gene expression data do not leverage information related to gene splicing, despite the fact that splicing is a fundamental feature of eukaryotic gene expression.
Zifeng Wang +11 more
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Investigating isoform switching in RHBDF2 and its role in neoplastic growth in breast cancer [PDF]
PeerJ, 2022 Background Breast cancer is the second leading cause of cancer-related deaths globally, and its prevalence rates are increasing daily. In the past, studies predicting therapeutic drug targets for cancer therapy focused on the assumption that one gene is ...
Mehar Masood +5 more
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