Tag Archives: alternative splicing

An open challenge that merges the efforts of the International Cancer Genome Consortium, The Cancer Genome Atlas, and the NCI Cloud Pilots with Sage Bionetworks and the open science DREAM Challenge community Scientists from around the world have announced a ...

Although RNA-Seq data provide unprecedented isoform-level expression information, detection of alternative isoform regulation (AIR) remains difficult, particularly when working with an incomplete transcript annotation. Researchers at the National Human Genome Research Institute introduce JunctionSeq, a new method that builds on the ...

Precise spatiotemporal regulation of splicing is mediated by splicing cis-elements on pre-mRNA. Single-nucleotide variations (SNVs) affecting intronic cis-elements possibly compromise splicing, but no efficient tool has been available to identify them. Following an effect-size analysis of each intronic nucleotide on ...

Cancer is a disease of the genome caused by oncogene activation and tumor suppressor gene inhibition. Deep sequencing studies including large consortia such as TCGA and ICGC identified numerous tumor-specific mutations not only in protein-coding sequences but also in non-coding ...

In cancer alternative RNA splicing represents one mechanism for flexible gene regulation, whereby protein isoforms can be created to promote cell growth, division and survival. Detecting novel splice junctions in the cancer transcriptome may reveal pathways driving tumourigenic events. In ...

Given that the majority of multi-exon genes generate diverse functional products, it is important to evaluate expression at the isoform level. Previous studies have demonstrated strong gene-level correlations between RNA sequencing (RNA-seq) and microarray platforms, but have not studied their ...

Next-generation RNA sequencing (RNA-seq) has been widely used to investigate alternative isoform regulations. Among them, alternative 3′ splice site (SS) and 5′ SS account for more than 30% of all alternative splicing (AS) events in higher eukaryotes. Recent studies have ...

RNA-Seq made possible the global identification of fusion transcripts, i.e. “chimeric RNAs”. Even though various software packages have been developed to serve this purpose, they behave differently in different datasets provided by different developers. It is important for both users, ...

Understanding the occurrence and regulation of alternative splicing (AS) is a key task towards explaining the regulatory processes that shape the complex transcriptomes of higher eukaryotes. With the advent of high-throughput sequencing of RNA (RNA-Seq), the diversity of AS transcripts ...

RNA-seq data analysis has revealed abundant alternative splicing in eukaryotic mRNAs. However, splicing is only one of many processing events that transcripts may undergo during their lifetime. Researchers from the Institute for Integrative Biology of the Cell, CNRS present here ...