Here we present a method, Altrans, for discovery of alternative splicing quantitative trait loci (asQTLs). To assess the performance of Altrans, we compared it to Cufflinks and MISO in simulations and Cufflinks for asQTL discovery. Simulations show that in the presence of unannotated transcripts...
The posterior probability that alternative splicing ofATP11Ain lung and COVID-19 outcomes shared a single causal signal in the 1 Mb locus around thecis-sQTL was 1.00 for critical illness, 1.00 for hospitalization due to COVID-19, and 0.98 for reported infection (Supplementary Fig.2A, Supple...
Identification of genetic variants associated with alternative splicing using sQTLseekeR. Nat. Commun. 5, 4698 (2014). Article CAS PubMed Google Scholar Yang, Y. et al. SNP2APA: a database for evaluating effects of genetic variants on alternative polyadenylation in human cancers. Nucleic Acids...
Understanding the consequences of individualtranscriptomevariation is fundamental to deciphering human biology and disease. We implement a statistical framework to quantify the contributions of 21 individual traits as drivers of gene expression and alternative splicing variation across 46 human tissues and 781...
Analysis of gene expression and alternative splicing (AS) will help speed gene identification and understand the role of AS in deep rooting. Methods Rice varieties displaying extreme ratio of deep rooting (RDR) were grown in nutrient solutions. RNA-seq analysis was conducted using StringTie, SUPPA...
Keywords: RNA-seq, alternative splicing, sQTL, exon, generalized linear mixed model Background Alternative splicing (AS) is the process by which exons from precursor mRNA transcripts are differentially included during splicing, resulting in different mature mRNA isoforms from a single gene locus [1]...
and reference binned distributions, the modality of reference binned distribution with the smallest distance was assigned. Thus, we designated genes into different modalities for each GABAergic neuron type (Fig.6a). For instance, the geneTardbpwith critical roles in splicing in neurons exhibits the ...
Furthermore, many DE and DS genes could be mapped to cis-acting QTL, arguing that some of this regulatory divergence is genetically based. DE and DS genes were also more likely to be "hub genes" than their nondivergent counterparts, hinting that this regulatory variation may have a variety ...
We then developed methods for assessing changes in gene expression due to SNP from those due to alternative splicing. Finally, we map potential genetic loci that control the alternative splicing (asQTL).Chen, LangDissertations & Theses - Gradworks...
Alternative splicing is central to metazoan gene regulation, but the regulatory mechanisms are incompletely understood. Here, we show that G-quadruplex (G4) motifs are enriched ~3-fold near splice junctions. The importance of G4s in RNA is emphasised by