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Psichomics: graphical application for alternative splicing quantification and analysis.

ABSTRACT: Alternative pre-mRNA splicing generates functionally distinct transcripts from the same gene and is involved in the control of multiple cellular processes, with its dysregulation being associated with a variety of pathologies. The advent of next-generation sequencing has enabled global studies of alternative splicing in different physiological and disease contexts. However, current bioinformatics tools for alternative splicing analysis from RNA-seq data are not user-friendly, disregard available exon-exon junction quantification or have limited downstream analysis features. To overcome such limitations, we have developed psichomics, an R package with an intuitive graphical interface for alternative splicing quantification and downstream dimensionality reduction, differential splicing and gene expression and survival analyses based on The Cancer Genome Atlas, the Genotype-Tissue Expression project, the Sequence Read Archive project and user-provided data. These integrative analyses can also incorporate clinical and molecular sample-associated features. We successfully used psichomics in a laptop to reveal alternative splicing signatures specific to stage I breast cancer and associated novel putative prognostic factors.

SUBMITTER: Saraiva-Agostinho N

PROVIDER: S-EPMC6344878 | biostudies-other | 2019 Jan

REPOSITORIES: biostudies-other

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psichomics: graphical application for alternative splicing quantification and analysis.

Saraiva-Agostinho Nuno N Barbosa-Morais Nuno L NL

Nucleic acids research 20190101 2

Alternative pre-mRNA splicing generates functionally distinct transcripts from the same gene and is involved in the control of multiple cellular processes, with its dysregulation being associated with a variety of pathologies. The advent of next-generation sequencing has enabled global studies of alternative splicing in different physiological and disease contexts. However, current bioinformatics tools for alternative splicing analysis from RNA-seq data are not user-friendly, disregard available ...[more]

PMID: 30277515

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Project description:BackgroundClassic epidemic curves - counts of daily events or cumulative events over time -emphasise temporal changes in the growth or size of epidemic outbreaks. Like any graph, these curves have limitations: they are impractical for comparisons of large and small outbreaks or of asynchronous outbreaks, and they do not display the relative growth rate of the epidemic. Our aim was to propose two additional graphical displays for the monitoring of epidemic outbreaks that overcome these limitations.MethodsThe first graph shows the growth of the epidemic as a function of its size; specifically, the logarithm of new cases on a given day, N(t), is plotted against the logarithm of cumulative cases C(t). Logarithm transformations facilitate comparisons of outbreaks of different sizes, and the lack of a time scale overcomes the need to establish a starting time for each outbreak. Notably, on this graph, exponential growth corresponds to a straight line with a slope equal to one. The second graph represents the logarithm of the relative rate of growth of the epidemic over time; specifically, log10(N(t)/C(t-1)) is plotted against time (t) since the 25th event. We applied these methods to daily death counts attributed to COVID-19 in selected countries, reported up to June 5, 2020.ResultsIn most countries, the log(N) over log(C) plots showed initially a near-linear increase in COVID-19 deaths, followed by a sharp downturn. They enabled comparisons of small and large outbreaks (e.g., Switzerland vs UK), and identified outbreaks that were still growing at near-exponential rates (e.g., Brazil or India). The plots of log10(N(t)/C(t-1)) over time showed a near-linear decrease (on a log scale) of the relative growth rate of most COVID-19 epidemics, and identified countries in which this decrease failed to set in in the early weeks (e.g., USA) or abated late in the outbreak (e.g., Portugal or Russia).ConclusionsThe plot of log(N) over log(C) displays simultaneously the growth and size of an epidemic, and allows easy identification of exponential growth. The plot of the logarithm of the relative growth rate over time highlights an essential parameter of epidemic outbreaks.

Project description:BACKGROUND: GABA has important functions in brain plasticity related processes like memory, learning, locomotion and during the development of the nervous system. It is synthesized by the glutamic acid decarboxylase (GAD). There are two isoforms of GAD, GAD1 and GAD2, which are encoded by different genes. During embryonic development the transcription of GAD1 mRNA is regulated by alternative splicing and several alternative transcripts were distinguished in human, mouse and rat. Despite the fact that the structure of GAD1 gene has been extensively studied, knowledge of its exact structural organization, alternative promoter usage and splicing have remained incomplete. RESULTS: In the present study we report the identification and characterization of novel GAD1 splicing isoforms (GenBank: KM102984, KM102985) by analyzing genomic and mRNA sequence data using bioinformatics, cloning and sequencing. Ten mRNA isoforms are generated from GAD1 gene locus by the combined actions of utilizing different promoters and alternative splicing of the coding exons. Using RT-PCR we found that GAD1 isoforms share similar pattern of expression in different mouse tissues and are expressed early during development. Quantitative RT-PCR was used to investigate the expression of GAD1 isoforms and GAD2 in olfactory bulb, cortex, medial and lateral striatum, hippocampus and cerebellum of adult mouse. Olfactory bulb showed the highest expression of GAD1 transcripts. Isoforms 1/2 are the most abundant forms. Their expression is significantly higher in the lateral compared to the medial striatum. Isoforms 3/4, 5/6, 7/8 and 9/10 are barely detectable in all investigated regions except of the high expression in olfactory bulb. When comparing GAD1 expression with GAD2 we found that Isoforms 1/2 are the predominant isoforms. In situ hybridization confirmed the predominant expression of Isoforms 7/8 and 9/10 in the olfactory bulb and revealed their weak expression in hippocampus, cerebellum and some other areas known to express GAD1. CONCLUSIONS: Generation of ten splicing isoforms of GAD1 was described including two so far uncharacterized transcripts. GAD1 splicing isoforms producing the shorter, enzymatically inactive GAD25 protein are expressed at very low level in adult mouse brain except in the olfactory bulb that is associated with neurogenesis and synaptic plasticity even during adulthood.

Dataset Information

Psichomics: graphical application for alternative splicing quantification and analysis.

Publications

psichomics: graphical application for alternative splicing quantification and analysis.

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