scRNA-Explorer:用于单细胞 RNA-seq 数据分析的终端用户在线工具,具有基因相关性和数据过滤功能

IF 4.7 2区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Journal of Molecular Biology Pub Date : 2024-09-01 DOI:10.1016/j.jmb.2024.168654
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摘要

在大多数单细胞 RNA 测序(scRNA-seq)下游分析管道中,都采用了降维和特征选择等技术来解决数据的高维性问题。这些方法包括将数据映射到低维空间,剔除信息量较少的基因,并找出最相关的特征。这一过程最终会减少用于下游分析的维数,进而加快大规模 scRNA-seq 数据的计算速度。大多数方法都是通过建立差异表达或共表达基因列表,从生物背景中分离出表征不同细胞或研究条件的基因。scRNA-Explorer 利用:(i) 通过网络界面以交互方式过滤掉无信息的细胞;(ii) 基因相关性分析,并额外评估这些相关性的生物学重要性;(iii) 对相关基因进行基因富集分析,以发现基因对特定功能的影响。我们开发了一个管道来解决上述问题。scRNA-Explorer 管道允许用户以交互方式查询 scRNA 序列数据集,通过基因表达相关性探索相关基因的可能功能。scRNA-Explorer 的访问网址为 https://bioinformatics.med.uoc.gr/shinyapps/app/scrnaexplorer。
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scRNA-Explorer: An End-user Online Tool for Single Cell RNA-seq Data Analysis Featuring Gene Correlation and Data Filtering

In the majority of downstream analysis pipelines for single-cell RNA sequencing (scRNA-seq), techniques like dimensionality reduction and feature selection are employed to address the problem of high-dimensional nature of the data. These approaches involve mapping the data onto a lower-dimensional space, eliminating less informative genes, and pinpointing the most pertinent features. This process ultimately leads to a reduction in the number of dimensions used for downstream analysis, which in turn speeds up the computation of large-scale scRNA-seq data. Most approaches are directed to isolate from biological background the genes characterizing different cells and or the condition under study by establishing lists of differentially expressed or coexpressed genes. Herein, we present scRNA-Explorer an open-source online tool for simplified and rapid scRNA-seq analysis designed with the end user in mind. scRNA-Explorer utilizes: (i) Filtering out uninformative cells in an interactive manner via a web interface, (ii) Gene correlation analysis coupled with an extra step of evaluating the biological importance of these correlations, and (iii) Gene enrichment analysis of correlated genes in order to find gene implication in specific functions. We developed a pipeline to address the above problem. The scRNA-Explorer pipeline allows users to interrogate in an interactive manner scRNA-sequencing data sets to explore via gene expression correlations possible function(s) of a gene of interest. scRNA-Explorer can be accessed at https://bioinformatics.med.uoc.gr/shinyapps/app/scrnaexplorer.

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来源期刊
Journal of Molecular Biology
Journal of Molecular Biology 生物-生化与分子生物学
CiteScore
11.30
自引率
1.80%
发文量
412
审稿时长
28 days
期刊介绍: Journal of Molecular Biology (JMB) provides high quality, comprehensive and broad coverage in all areas of molecular biology. The journal publishes original scientific research papers that provide mechanistic and functional insights and report a significant advance to the field. The journal encourages the submission of multidisciplinary studies that use complementary experimental and computational approaches to address challenging biological questions. Research areas include but are not limited to: Biomolecular interactions, signaling networks, systems biology; Cell cycle, cell growth, cell differentiation; Cell death, autophagy; Cell signaling and regulation; Chemical biology; Computational biology, in combination with experimental studies; DNA replication, repair, and recombination; Development, regenerative biology, mechanistic and functional studies of stem cells; Epigenetics, chromatin structure and function; Gene expression; Membrane processes, cell surface proteins and cell-cell interactions; Methodological advances, both experimental and theoretical, including databases; Microbiology, virology, and interactions with the host or environment; Microbiota mechanistic and functional studies; Nuclear organization; Post-translational modifications, proteomics; Processing and function of biologically important macromolecules and complexes; Molecular basis of disease; RNA processing, structure and functions of non-coding RNAs, transcription; Sorting, spatiotemporal organization, trafficking; Structural biology; Synthetic biology; Translation, protein folding, chaperones, protein degradation and quality control.
期刊最新文献
Editorial Board Outside Front Cover Assembly of the human multi-tRNA synthetase complex through leucine zipper motifs. Corrigendum to “The Role of ATG9 Vesicles in Autophagosome Biogenesis” [J. Mol. Biol. 436(15) (2024) 168489] Structural studies on Mycobacterial NudC reveal a class of zinc independent NADH pyrophosphatase.
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