WormBase 2024: status and transitioning to Alliance infrastructure

Genetics, Год журнала: 2024, Номер 227(1)

Опубликована: Апрель 4, 2024

Abstract WormBase has been the major repository and knowledgebase of information about genome genetics Caenorhabditis elegans other nematodes experimental interest for over 2 decades. We have 3 goals: to keep current with fast-paced C. research, provide better integration resources, be sustainable. Here, we discuss state as well progress plans moving core infrastructure Alliance Genome Resources (the Alliance). As an member, will continue interact community, develop new features needed, curate key from literature large-scale projects.

Язык: Английский

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A genome-wide scan of non-coding RNAs and enhancers for refractive error and myopia

Human Genetics, Год журнала: 2025, Номер unknown

Опубликована: Янв. 8, 2025

Refractive error (RE) and myopia are complex polygenic conditions with the majority of genome-wide associated genetic variants in non-exonic regions. Given this, onset during childhood, gene-regulation is expected to play an important role its pathogenesis. This prompted us explore beyond traditional gene finding approaches. We performed a association study between non-coding RNAs enhancers, RE myopia. obtained single-nucleotide polymorphisms (SNPs) microRNA (miRNA) genes, miRNA-binding sites, long genes (lncRNAs) enhancers from publicly available databases: miRNASNPv2, PolymiRTS, VISTA Enhancer Browser, FANTOM5 lncRNASNP2. investigated whether SNPs overlapping these elements were leveraged large GWAS meta-analysis (N = 160,420). With risk scores (GRSs) per element, we joint effect on RE, axial length (AL)/corneal radius (CR), AL progression independent child cohort, Generation R Study 3638 children). constructed score for biological plausibility SNP highly confident sites chromatin accessible found that two miRNA 14 81 lncRNA regions 54 myopia-associated loci. GRSs significantly AL/CR progression. lncRNAs all miRNAs not any ocular biometric measurement. showed suggestive but inconsistent significance. prioritized candidate binding future functional validation. Pathways target host ranked included eye development (BMP4, MPPED2), neurogenesis (DDIT4, NTM), extracellular matrix (ANTXR2, BMP3), photoreceptor metabolism (DNAJB12), morphogenesis (CHDR1), neural signaling (VIPR2) TGF-beta (ANAPC16). first large-scale Enhancers could be importance as they childhood provide blueprint validation by prioritizing enhancers.

Язык: Английский

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Selecting genes for analysis using historically contingent progress: from RNA changes to protein–protein interactions

Nucleic Acids Research, Год журнала: 2025, Номер 53(1)

Опубликована: Янв. 7, 2025

Abstract Progress in biology has generated numerous lists of genes that share some property. But advancing from these to understanding their roles is slow and unsystematic. Here we use RNA silencing Caenorhabditis elegans illustrate an approach for prioritizing detailed study given limited resources. The partially subjective relationships between forged by both deduced functional relatedness biased progress the field were captured as mutual information used cluster frequently identified yet remain understudied. Some proteins encoded understudied are predicted physically interact with known regulators silencing, suggesting feedback regulation. Predicted interactions act other processes clustering studied among most perturbed suggest regulatory links connecting like cell cycle asymmetric division. Thus, gene products altered when a process could be acting restore homeostasis, which provides way sequencing identify candidate protein–protein interactions. Together, analysis transcripts potential they encode help prioritize any process.

Язык: Английский

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Characterization and automated classification of sentences in the biomedical literature: a case study for biocuration of gene expression and protein kinase activity

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Янв. 8, 2025

Biological knowledgebases are essential resources for biomedical researchers, providing ready access to gene function and genomic data. Professional, manual curation of knowledgebases, however, is labor-intensive thus high-performing machine learning methods that improve biocuration efficiency needed. Here we report on sentence-level classification identify biocuration-relevant sentences in the full text published references two data types: expression protein kinase activity. We performed a detailed characterization from WormBase bibliography used this define three tasks classifying as either 1) fully curatable, 2) partially or 3) all language-related. evaluated various (ML) models applied these found GPT BioBERT achieve highest average performance, resulting F1 performance scores ranging 0.89 0.99 depending upon task. Our findings demonstrate feasibility extracting text. Integrating into professional workflows, such those by Alliance Genome Resources ACKnowledge community platform, might well facilitate efficient accurate annotation literature.

Язык: Английский

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Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database

Database, Год журнала: 2025, Номер 2025

Опубликована: Янв. 1, 2025

Abstract The Rat Genome Database (RGD) is a multispecies knowledgebase which integrates genetic, multiomic, phenotypic, and disease data across 10 mammalian species. To support cross-species, multiomics studies to enhance expand on manually extracted from the biomedical literature by RGD team of expert curators, imports multiple sources. These include major databases substantial number domain-specific resources, as well direct submissions individual researchers. incorporation these diverse datatypes handled growing list automated import, export, processing, quality control pipelines. This article outlines development over time standardized infrastructure for pipelines with summary key design decisions focus lessons learned.

Язык: Английский

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Molecular characterization of the heterogeneity of satellite cell populations isolated from an individual Turkey pectoralis major muscle

Frontiers in Physiology, Год журнала: 2025, Номер 16

Опубликована: Фев. 20, 2025

Satellite cells (SCs) are myogenic stem responsible for post hatch muscle growth and the regeneration of fibers. not a homogenous population within have variable rates proliferation differentiation even single fiber type like turkey pectoralis major muscle. In this study, satellite cell clones derived from same with different were compared. The classified as either fast-growing (early clone) or slow-growing (late SCs. To thoroughly examine molecular differences between these two groups, RNA sequencing was conducted to compare their transcriptomes following 72 h proliferation. Principal Component Analysis confirmed that transcriptomic profiles early- late-clones markedly distinct. Differential gene expression analysis identified over 5,300 genes significantly differentially expressed groups cells. Gene ontology showed highly in early fundamental aspects biology, including tissue development structural maturation. Conversely, upregulated late involved cell-cell communication, extracellular matrix interactions, signal ligand activity, cytokine activity-key components forming an niche essential functional maintenance. Further examination specific categories such structure indicated significant patterns late-clones. These findings highlight genetic diversity SCs turkeys. distinct roles populations indicate balance them is necessary preserving normal physiological functions

Язык: Английский

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Synaptic vesicle glycoprotein 2 enables viable aneuploidy following centrosome amplification

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Фев. 20, 2025

Abstract Amplified centrosome number causes genomic instability, most severely through division into more than two aneuploid daughter cells (multipolar mitosis). Several mechanisms that suppress multipolar have been uncovered, yet favor viable are poorly understood. To uncover factors promote viability in with frequent amplification and division, we conducted an unbiased Drosophila genetic screen. In 642 mutagenized lines, exploited the ability of intestinal papillar to form function despite divisions. Our top hit is unnamed gene, CG3168 . We name this gene synaptic vesicle glycoprotein 2 , reflecting homology human Synaptic Vesicle Glycoprotein (SV2) proteins. GFP-tagged SV2 localizes plasma membrane. amplified centrosomes, positions membrane-adjacent which prevents severe errors chromosome alignment segregation. results membrane-based regulation reveal a novel vulnerability common cancer properties.

Язык: Английский

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Mapping shared and unique features in spatial transcriptomics through multivariate curve resolution

Microchemical Journal, Год журнала: 2025, Номер unknown, С. 113189 - 113189

Опубликована: Фев. 1, 2025

Язык: Английский

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Whole-exome sequencing reveals sex difference in the genetic architecture of high myopia

Journal of Medical Genetics, Год журнала: 2025, Номер unknown, С. jmg - 110467

Опубликована: Март 12, 2025

Background High myopia (HM) is one of the leading causes visual impairment and blindness worldwide. To understand sex difference in genetic architecture HM, which may contribute to understanding HM aetiology help further realisation precision medicine for HM. Methods We performed sex-stratified exome-wide association studies (ExWAS) with n (males)=7492 (females)=8090, along gene- pathway-based tests correlation analyses clarify variants, genes molecular pathways that relate a sex-specific manner. Results In our ExWAS, we identified male-specific gene, CHRNB1 (Z females =1.382, P =0.083; Z males =4.029, =2.80×10 −05 ; =0.003), was associated higher risk scores than females. Rare variant burden showed significant excess rare protein-truncating variants among -related pathways, including cell-cell signalling muscle structure development. Sex-based differences gene expression within -enriched ciliary body cells were observed; specifically, increased mitochondrial metabolism-related antioxidant Functional metabolism confirmed male-derived H1 female-derived H9 human embryonic stem cell lines, specifically exhibiting dysregulation organisation respiratory chain complex assembly after knockdown. Conclusion Together, study provides insight into highlights ’s role pathogenesis males.

Язык: Английский

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Saccharomyces Genome Database: Advances in Genome Annotation, Expanded Biochemical Pathways, and Other Key Enhancements

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Сен. 20, 2024

ABSTRACT Budding yeast ( Saccharomyces cerevisiae ) is the most extensively characterized eukaryotic model organism and has long been used to gain insight into fundamentals of genetics, cellular biology, functions specific genes proteins. The Genome Database (SGD) a scientific resource that provides information about genome biology S. . For more than 30 years, SGD maintained genetic nomenclature, chromosome maps, functional annotation for budding along with search analysis tools explore these data. Here we describe recent updates at SGD, including two reference updates, expanded biochemical pathways representation, changes data files, other enhancements website user interface. These activities are part our continuing effort promote insights gained from enable discovery relationships between sequence gene products in fungi higher eukaryotes.

Язык: Английский

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