Upstream analysis of alternative splicing: a review of computational approaches to predict context-dependent splicing factors
Alternative splicing (AS) has shown to play a pivotal role in the development of diseases,
including cancer. Specifically, all the hallmarks of cancer (angiogenesis, cell immortality …
including cancer. Specifically, all the hallmarks of cancer (angiogenesis, cell immortality …
Discovery of novel splice forms and functional analysis of cancer‐specific alternative splicing in human expressed sequences
Q Xu, C Lee - Nucleic acids research, 2003 - academic.oup.com
We report here a genome‐wide analysis of alternative splicing in 2 million human expressed
sequence tags (ESTs), to identify splice forms that are up‐regulated in tumors relative to …
sequence tags (ESTs), to identify splice forms that are up‐regulated in tumors relative to …
Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context
Motivation: Alternative splicing is a major contributor to cellular diversity in mammalian
tissues and relates to many human diseases. An important goal in understanding this …
tissues and relates to many human diseases. An important goal in understanding this …
[HTML][HTML] Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis
The interpretation of genomic variants has become one of the paramount challenges in the
post-genome sequencing era. In this review we summarize nearly 20 years of research on …
post-genome sequencing era. In this review we summarize nearly 20 years of research on …
Combinations of histone modifications mark exon inclusion levels
Splicing is a complex process regulated by sequence at the classical splice sites and other
motifs in exons and introns with an enhancing or silencing effect. In addition, specific histone …
motifs in exons and introns with an enhancing or silencing effect. In addition, specific histone …
CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores
Background Splicing of genomic exons into mRNAs is a critical prerequisite for the accurate
synthesis of human proteins. Genetic variants impacting splicing underlie a substantial …
synthesis of human proteins. Genetic variants impacting splicing underlie a substantial …
Alterations of pre‐mRNA splicing in cancer
Recent genomewide analyses of alternative splicing (AS) indicate that up to 70% of human
genes may have alternative splice forms, suggesting that AS together with various …
genes may have alternative splice forms, suggesting that AS together with various …
ASCancer Atlas: a comprehensive knowledgebase of alternative splicing in human cancers
Alternative splicing (AS) is a fundamental process that governs almost all aspects of cellular
functions, and dysregulation in this process has been implicated in tumor initiation …
functions, and dysregulation in this process has been implicated in tumor initiation …
ASpedia: a comprehensive encyclopedia of human alternative splicing
Alternative splicing confers the human genome complexity by increasing the diversity of
expressed mRNAs. Hundreds or thousands of splicing regions have been identified through …
expressed mRNAs. Hundreds or thousands of splicing regions have been identified through …
Sequence information for the splicing of human pre-mRNA identified by support vector machine classification
Vertebrate pre-mRNA transcripts contain many sequences that resemble splice sites on the
basis of agreement to the consensus, yet these more numerous false splice sites are usually …
basis of agreement to the consensus, yet these more numerous false splice sites are usually …