Skip to main content
ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #408809
Research Project: Mapping Crop Genome Functions for Biology-Enabled Germplasm Improvement

Location: Plant, Soil and Nutrition Research

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

Author
item GEORGE, NANCY - Embl-Ebi
item FEXOVA, SILVIE - Embl-Ebi
item FUENTES, ALFONSO MUNOZ - Embl-Ebi
item MADRIGAL, PEDRO - Embl-Ebi
item BI, YALAN - Embl-Ebi
item IQBA, HAIDER - Embl-Ebi
item KUMBHAM, UPENDRA - European Molecular Biology Laboratory
item NOLTE, NADJA FRANCESCA - Embl-Ebi
item ZHAO, LINGYUN - Embl-Ebi
item PAPATHEODOROU, IRENE - European Molecular Biology Laboratory
item THANKI, ANIL - Embl-Ebi
item YU, IRIS - Embl-Ebi
item CALLES, JOSE C MARUGAN - Embl-Ebi
item ERDOS, KAROLY - Embl-Ebi
item VILMOVSKY, LIORA - Embl-Ebi
item KURRI, SANDEEP - Embl-Ebi
item VATHRAKOKOILI-POURNA, ANNA - Embl-Ebi
item OSUMI-SUTHERLAND, DAVID - Embl-Ebi
item PRAKASH, ANANTH - Embl-Ebi
item WANG, SHENGBO - Embl-Ebi
item TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item Ware, Doreen
item GOUTTE-GATTAT, DAMIAN - University Of Cambridge
item HU, YANHUI - Harvard Medical School
item BROWN, NICK - Harvard University
item PERRIMON, NORBERT - Harvard Medical School
item VIZCAINO, JUAN ANTONIO - Embl-Ebi
item BURDETT, TONY - Embl-Ebi
item TEICHMANN, SARAH - Wellcome Trust Sanger Institute
item BRAZMA, ALVIS - Embl-Ebi

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/30/2023
Publication Date: N/A
Citation: N/A
DOI: https://doi.org/10.1093/nar/gkad1021

Interpretive Summary: 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 databases for gene and protein expression and localisation of bulk RNAseq and single cell RNAseq experiments. We have included new data and species into Expression Atlas and Single Cell Expression Atlas. There is integration of community standards and resources in the updated expression atlases. We have also done the improvement of single cell analysis workflows and provided interactive cell level anatomograms and cell type gene expression heatmaps.

Technical 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 visualizations are available as interactive cell level anatomograms and cell type gene expression heatmaps.