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

Author:

George Nancy1ORCID,Fexova Silvie1,Fuentes Alfonso Munoz1,Madrigal Pedro1,Bi Yalan1,Iqbal Haider1,Kumbham Upendra1,Nolte Nadja Francesca1,Zhao Lingyun1,Thanki Anil S1,Yu Iris D1,Marugan Calles Jose C1,Erdos Karoly1,Vilmovsky Liora1,Kurri Sandeep R1,Vathrakokoili-Pournara Anna1ORCID,Osumi-Sutherland David1,Prakash Ananth1,Wang Shengbo1,Tello-Ruiz Marcela K2,Kumari Sunita2,Ware Doreen23ORCID,Goutte-Gattat Damien4ORCID,Hu Yanhui5ORCID,Brown Nick4,Perrimon Norbert56,Vizcaíno Juan Antonio1,Burdett Tony1,Teichmann Sarah7,Brazma Alvis1,Papatheodorou Irene1

Affiliation:

1. European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI , Hinxton CB10 1SD , UK

2. Cold Spring Harbour Laboratory , One Bungtown Road , Cold Spring Harbor , NY 11724 , USA

3. USDA ARS NEA, Plant Soil & Nutrition Laboratory Research Unit , Ithaca , NY 14853 , USA

4. FlyBase-Cambridge, Department of Physiology, Development and Neuroscience, University of Cambridge Downing Street , Cambridge CB2 3DY , UK

5. Perrimon Lab, Department of Genetics, Harvard Medical School , Boston MA 02115 , USA

6. FlyBase-Harvard Biological Laboratories, Harvard University , 16 Divinity Avenue , Cambridge , MA 02138 , USA

7. Wellcome Trust Sanger Institute. Wellcome Genome Campus , Hinxton CB10 1SA , UK

Abstract

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.

Funder

European Molecular Biology Laboratory

Wellcome Trust

BBSRC

Fly Cell Atlas

Gramene

Publisher

Oxford University Press (OUP)

Subject

Genetics

Reference35 articles.

1. Expression Atlas update: from tissues to single cells;Papatheodorou;Nucleic Acids Res.,2020

2. The BioStudies database—one stop shop for all data supporting a life sciences study;Sarkans;Nucleic Acids Res.,2018

3. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences;Perez-Riverol;Nucleic Acids Res.,2022

4. NCBI GEO: archive for functional genomics data sets–update;Barrett;Nucleic Acids Res.,2013

5. European Nucleotide Archive in 2016;Toribio;Nucleic Acids Res.,2017

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