Complex heatmap visualization

iMeta, Год журнала: 2022, Номер 1(3)

Опубликована: Авг. 1, 2022

Abstract Heatmap is a widely used statistical visualization method on matrix‐like data to reveal similar patterns shared by subsets of rows and columns. In the R programming language, there are many packages that make heatmaps. Among them, ComplexHeatmap package provides richest toolset for constructing highly customizable can easily establish connections between multisource information automatically concatenating adjusting list heatmaps as well complex annotations, which makes it applied in analysis fields, especially bioinformatics, find hidden structures data. this article, we give comprehensive introduction current state , including its modular design, rich functionalities, broad applications.

Язык: Английский

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Human microglial state dynamics in Alzheimer’s disease progression

Cell, Год журнала: 2023, Номер 186(20), С. 4386 - 4403.e29

Опубликована: Сен. 1, 2023

Altered microglial states affect neuroinflammation, neurodegeneration, and disease but remain poorly understood. Here, we report 194,000 single-nucleus transcriptomes epigenomes across 443 human subjects diverse Alzheimer's (AD) pathological phenotypes. We annotate 12 transcriptional states, including AD-dysregulated homeostatic, inflammatory, lipid-processing states. identify 1,542 AD-differentially-expressed genes, both microglia-state-specific disease-stage-specific alterations. By integrating epigenomic, transcriptomic, motif information, infer upstream regulators of cell gene-regulatory networks, enhancer-gene links, transcription-factor-driven state transitions. demonstrate that ectopic expression our predicted homeostatic-state activators induces homeostatic features in iPSC-derived microglia-like cells, while inhibiting inflammation can block inflammatory progression. Lastly, pinpoint the AD-risk genes differential their during AD Overall, provide insights underlying state-specific AD-stage-specific alterations at unprecedented resolution.

Язык: Английский

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EasyAmplicon: An easy‐to‐use, open‐source, reproducible, and community‐based pipeline for amplicon data analysis in microbiome research

iMeta, Год журнала: 2023, Номер 2(1)

Опубликована: Янв. 27, 2023

It is difficult for beginners to learn and use amplicon analysis software because there are so many tools choose from, all of them need multiple steps operation. Herein, we provide a cross-platform, open-source, community-supported pipeline EasyAmplicon. EasyAmplicon has most the modules needed an analysis, including data quality control, merging paired-end reads, dereplication, clustering or denoising, chimera detection, generation feature tables, taxonomic diversity compositional biomarker discovery, publication-quality visualization. includes more than 30 cross-platform R packages commonly used in field. All integrated into RStudio, which reduces learning costs, keeps flexibility process, facilitates personalized analysis. The maintained updated by authors editors WeChat official account "Meta-genome." Our team will regularly release latest tutorials both Chinese English, read feedback from users, help GitHub. can be deployed on various platforms, installation time less half hour. On ordinary laptop, whole process dozens samples completed within 3 h. available at GitHub (https://github.com/YongxinLiu/EasyAmplicon) Gitee (https://gitee.com/YongxinLiu/EasyAmplicon).

Язык: Английский

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The molecular cytoarchitecture of the adult mouse brain

Nature, Год журнала: 2023, Номер 624(7991), С. 333 - 342

Опубликована: Дек. 13, 2023

Abstract The function of the mammalian brain relies upon specification and spatial positioning diversely specialized cell types. Yet, molecular identities types their positions within individual anatomical structures remain incompletely known. To construct a comprehensive atlas in each structure, we paired high-throughput single-nucleus RNA sequencing with Slide-seq 1,2 —a recently developed transcriptomics method near-cellular resolution—across entire mouse brain. Integration these datasets revealed type composition neuroanatomical structure. Cell diversity was found to be remarkably high midbrain, hindbrain hypothalamus, most clusters requiring combination at least three discrete gene expression markers uniquely define them. Using data, framework for genetically accessing type, comprehensively characterized neuropeptide neurotransmitter signalling, elucidated region-specific specializations activity-regulated ascertained heritability enrichment neurological psychiatric phenotypes. These available as an online resource ( www.BrainCellData.org ), should find diverse applications across neuroscience, including construction new genetic tools prioritization specific circuits study diseases.

Язык: Английский

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Methylation of GPRC5A promotes liver metastasis and docetaxel resistance through activating mTOR signaling pathway in triple negative breast cancer

Drug Resistance Updates, Год журнала: 2024, Номер 73, С. 101063 - 101063

Опубликована: Фев. 1, 2024

This study aims to explore the function and mechanism of G Protein-coupled receptor class C group 5 member A (GPRC5A) in docetaxel-resistance liver metastasis breast cancer.

Язык: Английский

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OmicShare tools: A zero‐code interactive online platform for biological data analysis and visualization

iMeta, Год журнала: 2024, Номер 3(5)

Опубликована: Авг. 1, 2024

The OmicShare tools platform is a user-friendly online resource for data analysis and visualization, encompassing 161 bioinformatic tools. Users can easily track the progress of projects in real-time through an overview interface. has powerful interactive graphics engine that allows custom-tailored modification charts generated from analyses. visually appealing produced by improve interpretability meet requirements publication. It been acknowledged over 4000 publications available https://www.omicshare.com/tools/. Advances high-throughput sequencing technologies have resulted exponential increase volume biological data, creating significant challenges biologists analyzing extensive sets extracting meaningful insights them [1]. Typically, process initial acquisition to dissemination research findings involves three key stages: statistical analysis, creation charts, graphical enhancement. Many bioinformatics platforms or high throughput omics such as Majorbio Cloud [2], SangerBox [3], ImageGP [4], Wekemo [5], Evenn [6], Circos TBtools [7], complexHeatmap [8], ggVennDiagram [9], emerged. Most these were developed specific research, especially metagenomics transcriptomics, some provide solutions special problems. However, default graphic outputs often require fine-tuning using editing software (such Adobe Illustrator Photoshop) attain standard suitable Furthermore, many visualizing lack interfaces, which makes more complicated rather than simple mouse clicks [10]. To bridge this gap empower all researchers, including those without programming skills, smoothly navigate refinement one continuous workflow, we present (https://www.omicshare.com/tools/). This acts zero-code, portal streamlines granting researchers capability easy, adaptable, individualized exploration their data. suite robust collection utilities designed address multifaceted needs research. These span wide array functions, nucleic acid protein sequence gene function annotation, differential expression assessment, clustering evaluation, custom output creation. rich assortment offers full methods meticulous visualization depicted Figure 1A. Within framework, effortlessly carry out enrichment utilizing databases like Gene Ontology (GO), Kyoto Encyclopedia Genes Genomes (KEGG), Disease Ontology, Reactome. In addition, encompasses comprehensive set tests, correlation, variance, principal component (PCA), together with survival analysis. also facilitates production publication-ready graphics, heatmaps, Venn diagrams, scatter plots, cater standards scientific communication. suite, 129 offer features simplify imagery enable conceive visualizations. Examples include generating various specialized diagrams: grouped bar GO enrichment, correlation network composite plots Set Enrichment Analysis, PCA confidence intervals, diagrams comparing multiple cohorts, ridge displayed 1B–K. Additionally, integrated are exceptionally diverse detailed. For instance, KEGG tool does not just generate bubble (Figure 1E), it creates visuals circular 1H,K), offering variety ways display aid management adhere formatting analyses, format conversion utilities. streamline normalization standardization, facilitating IDs across different nomenclatures species accommodate transformation between "long" "wide" formats ease use enhance efficiency begin selecting best suits needs, uploading via interface, configuring necessary parameters launch 2A). successful arrange files fulfills tool. Each within accompanied sample file download users. encouraged templates own according avoid any mistakes 2B). Proper guidance provided setting parameter tool's instructional documentation. case utilities, users advised retain settings optimal results. feature monitoring system tracks task identifies errors. Once initiated, monitor its progression on project dashboard 2C). After completion, results immediate preview 2D). error, error-checking facility provides potential cause error. additional support, consult detailed documentation contact customer service team. proactively verify upon submission. Failure criteria will prevent initiation, triggering helpful error prompt. support formats, ensuring broad compatibility common types, FASTA files, tab-separated comma-separated value text Excel spreadsheets. possess advanced engine, crafted JavaScript dynamic chart customization community. presents range be modified allowing tweaks elements axes, fonts, themes, color schemes. selection predefined schemes, spanning 23 gradient colors 15 categorized palettes, added option concoct if defaults unsatisfactory. diagram tool, adjustments readily accessible, enabling alter visual aspects nodes edges, shape, size, color, transparency, label style, line thickness, curvature, style savable, swift reinstatement previous configurations revisiting interface transitioning tasks. By default, styles calibrated publication standards, produce presentation-ready minimal effort. Visual primed inclusion academic manuscripts, conforming quality publications. afforded flexibility personalize elements, refining preset suit preferences. supports export both bitmap images (JPG, PNG, BMP, TIF) vector (PDF, SVG), latter further modifications Illustrator, Inkscape, CorelDRAW. serves zero-coding, interactive, providing standards. facilitate seamless integration into scholarly articles mitigating steep learning curve commonly associated complex software. renowned heatmaps [11, 12], performing pathway analyses [13-15], conducting [16-18], [19, 20]. Since April 2016, garnered citations SCI-indexed papers. evolution characterized enhancements expansions. Despite tools, certain exhibit incomplete categorization, necessitating optimization adjustment. Future updates expected incorporate types analytical techniques, single-cell clinical Concurrently, efforts directed toward user settings, thereby enhancing accessibility limited expertise. platform, JavaScript, HTML, Bootstrap front-end development, responsive accessible On backend, web framework ThinkPHP employed preprocessing Some utilize R Python languages graphing, incorporating packages ggplot2, complexHeatmap, edgeR, DESeq2; integral evaluations high-quality Meanwhile, other leverage custom-developed drawing plugins, unique tailored representations directly based user-specific platform. Huangkai Zhou, Chuan Gao, Peng Ai conceived idea. Wenjie Huang Hongyan Mu functional modules interfaces. Jianzhou Chen, Gui Huang, Shimiao Hong completed process, cloud server development. wrote manuscript. Meiying Deng Zhou responsible revising All authors read final manuscript approved We would express our gratitude reports suggestions, well developers who technical project. declare no conflict interest. No animals humans involved study. at Supporting information (scripts, abstract, slides, videos, Chinese translated version, update materials) may found DOI iMeta Science https://www.imeta.science/.

Язык: Английский

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The best practice for microbiome analysis using R

Protein & Cell, Год журнала: 2023, Номер 14(10), С. 713 - 725

Опубликована: Май 2, 2023

With the gradual maturity of sequencing technology, many microbiome studies have published, driving emergence and advance related analysis tools. R language is widely used platform for data powerful functions. However, tens thousands packages numerous similar tools brought major challenges researchers to explore data. How choose suitable, efficient, convenient, easy-to-learn from has become a problem researchers. We organized 324 common classified them according application categories (diversity, difference, biomarker, correlation network, functional prediction, others), which could help quickly find relevant analysis. Furthermore, we systematically sorted integrated (phyloseq, microbiome, MicrobiomeAnalystR, Animalcules, microeco, amplicon) analysis, summarized advantages limitations, will appropriate Finally, thoroughly reviewed most content in formed suitable pipeline This paper accompanied by hundreds examples with 10,000 lines codes GitHub, can beginners learn, also analysts compare test different sorts providing an important theoretical basis practical reference development better future. All code available at GitHub github.com/taowenmicro/EasyMicrobiomeR.

Язык: Английский

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Pesticide Residues in French Soils: Occurrence, Risks, and Persistence

Environmental Science & Technology, Год журнала: 2023, Номер 57(20), С. 7818 - 7827

Опубликована: Май 12, 2023

Contamination of the environment by pesticide residues is a growing concern given their widespread presence in and effects on ecosystems. Only few studies have addressed occurrence pesticides soils, results highlighted need for further research persistence risks induced those substances. We monitored 111 (48 fungicides, 36 herbicides, 25 insecticides and/or acaricides, two safeners) 47 soils sampled across France under various land uses (arable lands, vineyards, orchards, forests, grasslands, brownfields). Pesticides were found 98% sites (46 sampled), including untreated areas such as organic fields, brownfields, with up to 33 different substances detected one sample, mostly fungicides herbicides. The concentrations herbicides highest glyphosate, its transformation product, AMPA, contributed 70% cumulative Risk assessment underlined moderate high risk earthworms arable attributed acaricides. Finally, comparison application farmers underlines some long after supposed 90% degradation at higher than predicted environmental concentrations, leading questions real soils.

Язык: Английский

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Multiomic spatial landscape of innate immune cells at human central nervous system borders

Nature Medicine, Год журнала: 2023, Номер 30(1), С. 186 - 198

Опубликована: Дек. 20, 2023

Abstract The innate immune compartment of the human central nervous system (CNS) is highly diverse and includes several immune-cell populations such as macrophages that are frequent in brain parenchyma (microglia) less numerous at interfaces CNS-associated (CAMs). Due to their scantiness particular location, little known about presence temporally spatially restricted CAM subclasses during development, health perturbation. Here we combined single-cell RNA sequencing, time-of-flight mass cytometry spatial transcriptomics with fate mapping advanced immunohistochemistry comprehensively characterize CNS over 356,000 analyzed transcriptomes from 102 individuals. We also provide a comprehensive analysis resident engrafted myeloid cells brains 15 individuals peripheral blood stem cell transplantation, revealing compartment-specific engraftment rates across different interfaces. Integrated multiomic high-resolution transcriptome anatomically dissected glioblastoma samples shows regionally distinct cell-type distributions driven by hypoxia. Notably, glioblastoma-associated hypoxia response was physiological fetal microglia CAMs. Our results highlight diversity periphery insights into complexities brain’s system.

Язык: Английский

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A concerted neuron–astrocyte program declines in ageing and schizophrenia

Nature, Год журнала: 2024, Номер 627(8004), С. 604 - 611

Опубликована: Март 6, 2024

Abstract Human brains vary across people and over time; such variation is not yet understood in cellular terms. Here we describe a relationship between people’s cortical neurons astrocytes. We used single-nucleus RNA sequencing to analyse the prefrontal cortex of 191 human donors aged 22–97 years, including healthy individuals with schizophrenia. Latent-factor analysis these data revealed that, whose more strongly expressed genes encoding synaptic components, astrocytes distinct functions for synthesizing cholesterol, an astrocyte-supplied component membranes. call this neuron astrocyte program (SNAP). In schizophrenia ageing—two conditions that involve declines cognitive flexibility plasticity 1,2 —cells divested from SNAP: astrocytes, glutamatergic (excitatory) GABAergic (inhibitory) all showed reduced SNAP expression corresponding degrees. The astrocytic neuronal components both involved which genetic risk factors were concentrated. SNAP, varies quantitatively even among similar age, may underlie many aspects normal interindividual differences be important point convergence multiple kinds pathophysiology.

Язык: Английский

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