Expression Atlas update: insights from sequencing data at both bulk and single cell level

George, Nancy, Fexova, Silvie, Fuentes, Alfonso Munoz, Madrigal, Pedro, Bi, Yalan, Iqbal, Haider, Kumbham, Upendra, Nolte, Nadja Francesca, Zhao, Lingyun, Thanki, Anil S, Yu, Iris D, Marugan Calles, Jose C, Erdos, Karoly, Vilmovsky, Liora, Kurri, Sandeep R, Vathrakokoili-Pournara, Anna, Osumi-Sutherland, David, Prakash, Ananth, Wang, Shengbo, Tello-Ruiz, Marcela K, Kumari, Sunita, Ware, Doreen, Goutte-Gattat, Damien, Hu, Yanhui, Brown, Nick, Perrimon, Norbert, Vizcaíno, Juan Antonio, Burdett, Tony, Teichmann, Sarah, Brazma, Alvis, Papatheodorou, Irene (November 2023) Expression Atlas update: insights from sequencing data at both bulk and single cell level. Nucleic Acids Research (NAR). gkad1021. ISSN 0305-1048

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Abstract

Expression Atlas (www.ebi.ac.uk/gxa) and its newest counterpart the Single Cell Expression Atlas (www.ebi.ac.uk/gxa/sc) are EMBL-EBI's knowledgebases for gene and protein expression and localisation in bulk and at single cell level. These resources aim to allow users to investigate their expression in normal tissue (baseline) or in response to perturbations such as disease or changes to genotype (differential) across multiple species. Users are invited to search for genes or metadata terms across species or biological conditions in a standardised consistent interface. Alongside these data, new features in Single Cell Expression Atlas allow users to query metadata through our new cell type wheel search. At the experiment level data can be explored through two types of dimensionality reduction plots, t-distributed Stochastic Neighbor Embedding (tSNE) and Uniform Manifold Approximation and Projection (UMAP), overlaid with either clustering or metadata information to assist users' understanding. Data are also visualised as marker gene heatmaps identifying genes that help confer cluster identity. For some data, additional visualisations are available as interactive cell level anatomograms and cell type gene expression heatmaps.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA expression bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics
CSHL Authors:	Kumari, Sunita Ware, Doreen H. Tello-Ruiz, Marcella
Communities:	CSHL labs > Ware lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	22 November 2023
Date Deposited:	20 Dec 2023 18:56
Last Modified:	11 Apr 2024 13:46
PMCID:	PMC10767917
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/41334

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