Alternative splicing is known to remodel protein-protein interaction networks ("interactomes"), yet large-scale determination of isoform-specific interactions remains challenging. We present a domain-based method to predict the isoform interactome from the reference interactome. First, we construct the domain-resolved reference interactome by mapping known domain-domain interactions onto experi...

Cutaneous T-cell lymphoma (CTCL), a heterogeneous group of extranodal non-Hodgkin’s lymphoma. In this study, we sequenced skin T cells on single cell level from patients with mycosis fungoides (MF), the most common type CTCL, and segregated clonal malignant non-clonal bystander by natural clonality identifier – receptor (TCR). Based our attention-ANN, an artificial intelligent method, identifie...

Alternative splicing (AS) of messenger RNAs diversifies gene function by generating protein isoforms with different biological properties. Over 95% human genes are alternatively spliced, but the functional consequences most AS events still not known. Here, using long-read RNA sequencing, we identified 5,826 associated epidermal differentiation (percent spliced index >10%, FDR <0.01). were enric...

Calcium ions are an important intracellular regulator; increase in their concentration the cytoplasm plays a key role determining functional activity of platelets associated with platelet aggregation and release reaction. The main way to reduce free calcium is activation Ca2+-ATPases depositing structures plasma membrane, which cytoplasmic content due its reuptake depot (resequestration) Ca2+ f...

The Wilms' tumor gene WT1 consists of 10 exons and encodes a zinc finger transcription factor. There are four major WT1 isoforms resulting from alternative splicing at two sites, exon 5 (17AA) and exon 9 (KTS). All major WT1 isoforms are overexpressed in leukemia and solid tumors and play oncogenic roles such as inhibition of apoptosis, and promotion of cell proliferation, migration and invasio...

Maximum likelihood is a popular technique for isoform reconstruction. Here, we show that isoform reconstruction using short RNA-Seq reads by maximum likelihood is NP-hard.

Next-generation RNA sequencing (RNA-seq) technology has been widely used to assess full-length RNA isoform abundance in a highthroughput manner. RNA-seq data offer insight into gene expression levels and transcriptome structure, enabling us to better understand the regulation of gene expression and fundamental biological processes. Accurate quantification of RNA isoforms from RNA-seq data is a ...

Motivation Current bioinformatics methods to detect changes in gene isoform usage in distinct phenotypes compare the relative expected isoform usage in phenotypes. These statistics model differences in isoform usage in normal tissues, which have stable regulation of gene splicing. Pathological conditions, such as cancer, can have broken regulation of splicing that increases the heterogeneity of...

Nramp2/DMT1 is a transmembrane proton-coupled Fe(2+) transporter. Two different mRNAs are generated by alternative splicing; isoform I contains an iron responsive element (IRE), whereas isoform II does not. They encode two proteins differing at their C-terminal end and by their subcellular localization. IRE-mediated stabilization of isoform I mRNA is thought to stimulate DMT1 expression in resp...