High-throughput short-read sequencing has revolutionized how transcriptomes are quantified and annotated. However, while Illumina short-read sequencers can be used to analyze entire transcriptomes down to the level of individual splicing events with great accuracy, they fall short of analyzing how ...
Read More »Almost every noncoding exon undergoes alternative splicing
The human transcriptome is so large, diverse, and dynamic that, even after a decade of investigation by RNA sequencing (RNA-seq), we have yet to resolve its true dimensions. RNA-seq suffers from an expression-dependent bias that impedes characterization of low-abundance transcripts. ...
Read More »Gene expression should be analyzed on the isoform level
Alternative usage of transcript isoforms from the same gene has been hypothesized as an important feature in cancers. However, differential usage of gene transcripts between conditions – isoform switching – has not been comprehensively characterized in and across cancer types. ...
Read More »Power analysis at the isoform level
RNA-Sequencing (RNA-Seq) has become a routine technology for investigating gene expression differences in comparative transcriptomic studies. Differential expression (DE) analysis of the isoforms of genes is just emerging now that expression (read counts) can be estimated with higher accuracy at ...
Read More »The Pitfalls of RNA-Seq Methodology
TP53 undergoes multiple RNA-splicing events, resulting in at least nine mRNA transcripts encoding at least 12 functionally different protein isoforms. Antibodies specific to p53 protein isoforms have proven difficult to develop, thus researchers must rely on the transcript information to ...
Read More »Phenotype prediction from alternative splicing and gene expression data
A central task of bioinformatics is to develop sensitive and specific means of providing medical prognoses from biomarker patterns. Common methods to predict phenotypes in RNA-Seq datasets utilize machine learning algorithms trained via gene expression. Isoforms, however, generated from alternative ...
Read More »Using big data, scientists discover biomarkers that could help give cancer patients better survival estimates
A SURVIV analysis of breast cancer isoforms developed at UCLA. Blue lines are associated with longer survival times, and magenta lines with shorter survival times. People with cancer are often told by their doctors approximately how long they have to ...
Read More »JunctionSeq – detection and visualization of differential splicing in RNA-Seq data
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 ...
Read More »BinPacker – Packing-Based De Novo Transcriptome Assembly from RNA-Seq Data
High-throughput RNA-seq technology has provided an unprecedented opportunity to reveal the very complex structures of transcriptomes. However, it is an important and highly challenging task to assemble vast amounts of short RNA-seq reads into transcriptomes with alternative splicing isoforms. Now, ...
Read More »NMFP – a non-negative matrix factorization based preselection method to identify mRNA isoforms from RNA-seq data
The advent of next-generation RNA sequencing (RNA-seq) has greatly advanced transcriptomic studies, including system-wide identification and quantification of mRNA isoforms under various biological conditions. A number of computational methods have been developed to systematically identify mRNA isoforms in a high-throughput ...
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