RhythmicDB: A Database of Predicted Multi-Frequency Rhythmic Transcripts.
Ontology highlight
ABSTRACT:
SUBMITTER: Castellana S
PROVIDER: S-EPMC9237250 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:BackgroundThe genetic prevalence of Pompe disease was estimated based on the proportion of individuals who have a causative genotype in a general population database. In addition, clinical severity for causative genotypes was assessed based on currently available locus-specific databases (LSDBs), which contain information on both genotype and clinical severity.MethodsGenetic variants in the GAA gene in the Genome Aggregation Database (gnomAD) (v2.1.1) were analyzed in combination with LSDBs of ClinVar, ClinGen Evidence Repository, Pompe disease GAA variant database, and the Pompe Registry. Carrier frequency (CF) and predicted genetic prevalence (pGP) were estimated.ResultsOf 7 populations, East Asian and African showed higher proportions of pathogenic or likely pathogenic variants (PLPVs) associated with classic infantile-onset Pompe disease. Total CF and pGP in the overall population were 1.3% (1 in 77) and 1:23,232, respectively. The highest pGP was observed in the East Asian population at 1:12,125, followed by Non-Finnish European (1:13,756), Ashkenazi Jewish (1:22,851), African/African-American (1:26,560), Latino/Admixed American (1:57,620), South Asian (1:93,087), and Finnish (1:1,056,444).ConclusionsPompe disease has a higher pGP (1:23,232) than earlier accepted (1:40,000). The pGP for Pompe disease was expectedly wide by population and consistent with previous reports based on newborn screening programs (approximately 1:10,000-1:30,000).
| S-EPMC7933537 | biostudies-literature
Project description:The use of high-throughput RNA sequencing technology (RNA-seq) allows whole transcriptome analysis, providing an unbiased and unabridged view of alternative transcript expression. Coupling splicing variant-specific expression with its functional inference is still an open and difficult issue for which we created the DataBase of Alternative Transcripts Expression (DBATE), a web-based repository storing expression values and functional annotation of alternative splicing variants. We processed 13 large RNA-seq panels from human healthy tissues and in disease conditions, reporting expression levels and functional annotations gathered and integrated from different sources for each splicing variant, using a variant-specific annotation transfer pipeline. The possibility to perform complex queries by cross-referencing different functional annotations permits the retrieval of desired subsets of splicing variant expression values that can be visualized in several ways, from simple to more informative. DBATE is intended as a novel tool to help appreciate how, and possibly why, the transcriptome expression is shaped. DATABASE URL: http://bioinformatica.uniroma2.it/DBATE/.
| S-EPMC5654372 | biostudies-literature
Project description:To assess how genomic information of the general population reflects probabilities of developing diseases and the differences in those probabilities among ethnic groups, a general population database was analyzed with an example of congenital hypothyroidism. Twelve candidate genes that follow an autosomal recessive inheritance pattern in congenital hypothyroidism (SLC5A5, TPO, TG, IYD, DUOXA2, DUOX2, TSHR, SLC26A7, GLIS3, FOXE1, TSHB, TRHR) in the gnomAD database (v2.1.1) were analyzed. The carrier frequency (CF) and predicted genetic prevalence (pGP) were estimated. The total CF in the overall population was 3.6%. DUOX2 showed the highest CF (1.8%), followed by TG (0.46%), TPO (0.44%), TSHR (0.31%), SLC26A7 (0.144%), DUOXA2 (0.141%), IYD (0.08%), SLC5A5 (0.06%), TRHR (0.059%), GLIS3 (0.059%), TSHB (0.04%), and FOXE1 (0%). The pGP in the overall population was 10.01 individuals per 100,000 births (1:9992). The highest pGP was in the East Asian population at 52.48 per 100,000 births (1:1905), followed by Finnish (35.96), Non-Finnish European (9.56), African/African American (4.0), Latino/Admixed American (3.89), South Asian (3.56), and Ashkenazi Jewish (1.81) groups. Comparing the pGP with the real incidence of congenital hypothyroidism, the pGP in East Asian populations was highly consistent with the real incidence.
| S-EPMC8228807 | biostudies-literature
Project description:Transcranial alternating current stimulation (tACS) has emerged as a promising tool for modulating cortical oscillations. In previous electroencephalogram (EEG) studies, tACS has been found to modulate brain oscillatory activity in a frequency-specific manner. However, the spatial distribution and hemodynamic response for this modulation remains poorly understood. Functional magnetic resonance imaging (fMRI) has the advantage of measuring neuronal activity in regions not only below the tACS electrodes but also across the whole brain with high spatial resolution. Here, we measured fMRI signal while applying tACS to modulate rhythmic visual activity. During fMRI acquisition, tACS at different frequencies (4, 8, 16, and 32 Hz) was applied along with visual flicker stimulation at 8 and 16 Hz. We analyzed the blood-oxygen-level-dependent (BOLD) signal difference between tACS-ON vs tACS-OFF, and different frequency combinations (e.g., 4 Hz tACS, 8 Hz flicker vs 8 Hz tACS, 8 Hz flicker). We observed significant tACS modulation effects on BOLD responses when the tACS frequency matched the visual flicker frequency or the second harmonic frequency. The main effects were predominantly seen in regions that were activated by the visual task and targeted by the tACS current distribution. These findings bridge different scientific domains of tACS research and demonstrate that fMRI could localize the tACS effect on stimulus-induced brain rhythms, which could lead to a new approach for understanding the high-level cognitive process shaped by the ongoing oscillatory signal.
| S-EPMC6141005 | biostudies-literature
Project description:Hot spots are energetically important residues at protein interfaces and they are not randomly distributed across the interface but rather clustered. These clustered hot spots form hot regions. Hot regions are important for the stability of protein complexes, as well as providing specificity to binding sites. We propose a database called HotRegion, which provides the hot region information of the interfaces by using predicted hot spot residues, and structural properties of these interface residues such as pair potentials of interface residues, accessible surface area (ASA) and relative ASA values of interface residues of both monomer and complex forms of proteins. Also, the 3D visualization of the interface and interactions among hot spot residues are provided. HotRegion is accessible at http://prism.ccbb.ku.edu.tr/hotregion.
| S-EPMC3245113 | biostudies-literature
Project description:High frequency oscillations (HFOs) are bursts of neural activity in the range of 80 Hz or higher, recorded from intracranial electrodes during epileptiform discharges. HFOs are a proposed biomarker of epileptic brain tissue and may also be useful for seizure forecasting. Despite such clinical utility of HFOs, the spatial context and neuronal activity underlying these local field potential (LFP) events remains unclear. We sought to further understand the neuronal correlates of ictal high frequency LFPs using multielectrode array recordings in the human neocortex and mesial temporal lobe during rhythmic onset seizures. These multiscale recordings capture single cell, multiunit, and LFP activity from the human brain. We compare features of multiunit firing and high frequency LFP from microelectrodes and macroelectrodes during ictal discharges in both the seizure core and penumbra (spatial seizure domains defined by multiunit activity patterns). We report differences in spectral features, unit-local field potential coupling, and information theoretic characteristics of high frequency LFP before and after local seizure invasion. Furthermore, we tie these time-domain differences to spatial domains of seizures, showing that penumbral discharges are more broadly distributed and less useful for seizure localization. These results describe the neuronal and synaptic correlates of two types of pathological HFOs in humans and have important implications for clinical interpretation of rhythmic onset seizures.
| S-EPMC7645614 | biostudies-literature
Project description:Fusion transcripts are chimeric RNAs generated as a result of fusion either at DNA or RNA level. These novel transcripts have been extensively studied in the case of human cancers but still remain underexamined in plants. In this study, we introduce the first plant-specific database of fusion transcripts named AtFusionDB (http://www.nipgr.res.in/AtFusionDB). This is a comprehensive database that contains the detailed information about fusion transcripts identified in model plant Arabidopsis thaliana. A total of 82 969 fusion transcript entries generated from 17 181 different genes of A. thaliana are available in this database. Apart from the basic information consisting of the Ensembl gene names, official gene name, tissue type, EricScore, fusion type, AtFusionDB ID and sample ID (e.g. Sequence Read Archive ID), additional information like UniProt, gene coordinates (together with the function of parental genes), junction sequence, expression level of both parent genes and fusion transcript may be of high utility to the user. Two different types of search modules viz. 'Simple Search' and 'Advanced Search' in addition to the 'Browse' option with data download facility are provided in this database. Three different modules for mapping and alignment of the query sequences viz. BLASTN, SW Align and Mapping are incorporated in AtFusionDB. This database is a head start for exploring the complex and unexplored domain of gene/transcript fusion in plants.
| S-EPMC6323297 | biostudies-literature
Project description:Motivated by applications in physical and biological sciences, we developed a Frequency Modulated Möbius (FMM) model to describe rhythmic patterns in oscillatory systems. Unlike standard symmetric sinusoidal models, FMM is a flexible parametric model that allows deformations to sinusoidal shape to accommodate commonly seen asymmetries in applications. FMM model parameters are easy to estimate and the model is easy to interpret complex rhythmic data. We illustrate FMM model in three disparate applications, namely, circadian clock gene expression, corticoptropin levels in depressed patients and the temporal light intensity patterns of distant stars. In each case, FMM model is demonstrated to be flexible, scientifically plausible and easy to interpret. Analysis of synthetic data derived from patterns of real data, suggest that FMM model fits the data very well both visually as well as in terms of the goodness of fit measure total mean squared error. An R language based software for implementing FMM model is available.
| S-EPMC6904729 | biostudies-literature
Project description:The search for radioprotectors is an ambitious goal with many practical applications. Particularly, the improvement of human radioresistance for space is an important task, which comes into view with the recent successes in the space industry. Currently, all radioprotective drugs can be divided into two large groups differing in their effectiveness depending on the type of exposure. The first of these is radioprotectors, highly effective for pulsed, and some types of relatively short exposure to irradiation. The second group consists of long-acting radioprotectors. These drugs are effective for prolonged and fractionated irradiation. They also protect against impulse exposure to ionizing radiation, but to a lesser extent than short-acting radioprotectors. Creating a database on radioprotectors is a necessity dictated by the modern development of science and technology. We have created an open database, Radioprotectors.org, containing an up-to-date list of substances with proven radioprotective properties. All radioprotectors are annotated with relevant chemical and biological information, including transcriptomic data, and can be filtered according to their properties. Additionally, the performed transcriptomics analysis has revealed specific transcriptomic profiles of radioprotectors, which should facilitate the search for potent radioprotectors.
| S-EPMC7467366 | biostudies-literature
Project description:Molecular markers are required in a broad spectrum of gene screening approaches, ranging from gene-mapping within traditional 'forward'-genetics approaches through QTL identification studies to genotyping and haplotyping studies. As we enter the post-genomics era, the need for genetic markers does not diminish, even in the species with fully sequenced genomes. PlantMarkers is a genetic marker database that contains a comprehensive pool of predicted molecular markers. We have adopted contemporary techniques to identify putative single nucleotide polymorphism (SNP), simple sequence repeat (SSR) and conserved orthologue set markers. A systematic approach to identify as broad a range of putative markers has been undertaken by screening the available openSputnik unigene consensus sequences from over 50 plant species. A web presence at http://markers.btk.fi provides functionality so that a user may search for species-specific markers on the basis of many specific criteria not limited to non-synonymous SNPs segregating between different varieties or measured polymorphic SSRs. Feedback forms are provided with all sequence entries to enable inclusion of, for example, map location for markers validated by the research community.
| S-EPMC540028 | biostudies-literature