Expression Atlas update: gene and protein expression in multiple species

被引：120

作者：

Moreno, Pablo ^{[1
]}

Fexova, Silvie ^{[1
]}

George, Nancy ^{[1
]}

Manning, Jonathan R. ^{[1
]}

Miao, Zhichiao ^{[1
]}

Mohammed, Suhaib ^{[1
]}

Munoz-Pomer, Alfonso ^{[1
]}

Fullgrabe, Anja ^{[1
]}

Bi, Yalan ^{[1
]}

Bush, Natassja ^{[1
]}

Iqbal, Haider ^{[1
]}

Kumbham, Upendra ^{[1
]}

Solovyev, Andrey ^{[1
]}

Zhao, Lingyun ^{[1
]}

Prakash, Ananth ^{[1
]}

Garcia-Seisdedos, David ^{[1
]}

Kundu, Deepti J. ^{[1
]}

Wang, Shengbo ^{[1
]}

Walzer, Mathias ^{[1
]}

Clarke, Laura ^{[1
]}

Osumi-Sutherland, David ^{[1
]}

Tello-Ruiz, Marcela Karey ^{[2
]}

Kumari, Sunita ^{[2
]}

Ware, Doreen ^{[2
,3
]}

Eliasova, Jana ^{[4
]}

Arends, Mark J. ^{[5
]}

Nawijn, Martijn C. ^{[6
]}

Meyer, Kerstin ^{[4
]}

Burdett, Tony ^{[1
]}

Marioni, John ^{[1
]}

Teichmann, Sarah ^{[4
]}

Vizcaino, Juan Antonio ^{[1
]}

Brazma, Alvis ^{[1
]}

Papatheodorou, Irene ^{[1
]}

机构：

[1] EMBL EBI, European Bioinformat Inst, European Mol Biol Lab, Wellcome Genome Campus, Hinxton, England

[2] CoId Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA

[3] USDA ARS NEA, Plant Soil & Nutr Lab Res Unit, Ithaca, NY 14853 USA

[4] Wellcome Sanger Inst, Wellcome Genome Campus, Hinxton, England

[5] Univ Edinburgh, Inst Genet & Canc, Edinburgh Pathol, Edinburgh, Midlothian, Scotland

[6] Univ Groningen, Univ Med Ctr Groningen, GRIAC Res Inst, Dept Pathol & Med Biol, Groningen, Netherlands

来源：

NUCLEIC ACIDS RESEARCH | 2022年 / 50卷 / D1期

基金：

英国生物技术与生命科学研究理事会; 英国惠康基金; 美国国家科学基金会;

关键词：

ARCHIVE;

D O I：

10.1093/nar/gkab1030

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The EMBL-EBI Expression Atlas is an added value knowledge base that enables researchers to answer the question of where (tissue, organism part, developmental stage, cell type) and under which conditions (disease, treatment, gender, etc) a gene or protein of interest is expressed. Expression Atlas brings together data from >4500 expression studies from >65 different species, across different conditions and tissues. It makes these data freely available in an easy to visualise form, after expert curation to accurately represent the intended experimental design, re-analysed via standardised pipelines that rely on open-source community developed tools. Each study's metadata are annotated using ontologies. The data are re-analyzed with the aim of reproducing the original conclusions of the underlying experiments. Expression Atlas is currently divided into Bulk Expression Atlas and Single Cell Expression Atlas. Expression Atlas contains data from differential studies (microarray and bulk RNA-Seq) and baseline studies (bulk RNA-Seq and proteomics), whereas Single Cell Expression Atlas is currently dedicated to Single Cell RNA-Sequencing (scRNA-Seq) studies. The resource has been in continuous development since 2009 and it is available at https://www.ebi.ac.uk/gxa.

引用

页码：D129 / D140

页数：12

共 37 条

[1] The COMPARE Data Hubs [J].

Amid, Clara ;

Pakseresht, Nima ;

Silvester, Nicole ;

Jayathilaka, Suran ;

Lund, Ole ;

Dynovski, Lukasz D. ;

Pataki, Balint A. ;

Visontai, David ;

Xavier, Basil Britto ;

Alako, Blaise T. F. ;

Belka, Ariane ;

Cisneros, Jose L. B. ;

Cotten, Matthew ;

Haringhuizen, George B. ;

Harrison, Peter W. ;

Hoper, Dirk ;

Holt, Sam ;

Hundahl, Camilla ;

Hussein, Abdulrahman ;

Kaas, Rolf S. ;

Liu, Xin ;

Leinonen, Rasko ;

Malhotra-Kumar, Surbhi ;

Nieuwenhuijse, David F. ;

Rahman, Nadim ;

Ribeiro, Carolina dos S. ;

Skiby, Jeffrey E. ;

Schmitz, Dennis ;

Steger, Jozsef ;

Szalai-Gindl, Janos M. ;

Thomsen, Martin C. F. ;

Caccio, Simone M. ;

Csabai, Istvan ;

Kroneman, Annelies ;

Koopmans, Marion ;

Aarestrup, Frank ;

Cochrane, Guy .

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2019,

[2] The international nucleotide sequence database collaboration [J].

Arita, Masanori ;

Karsch-Mizrachi, Ilene ;

Cochrane, Guy .

NUCLEIC ACIDS RESEARCH, 2021, 49 (D1) :D121-D124

[3] ArrayExpress update - from bulk to single-cell expression data [J].

Athar, Awais ;

Fullgrabe, Anja ;

George, Nancy ;

Iqbal, Haider ;

Huerta, Laura ;

Ali, Ahmed ;

Snow, Catherine ;

Fonseca, Nuno A. ;

Petryszak, Robert ;

Papatheodorou, Irene ;

Sarkans, Ugis ;

Brazma, Alvis .

NUCLEIC ACIDS RESEARCH, 2019, 47 (D1) :D711-D715

[4] NCBI GEO: archive for functional genomics data sets-update [J].

Barrett, Tanya ;

Wilhite, Stephen E. ;

Ledoux, Pierre ;

Evangelista, Carlos ;

Kim, Irene F. ;

Tomashevsky, Maxim ;

Marshall, Kimberly A. ;

Phillippy, Katherine H. ;

Sherman, Patti M. ;

Holko, Michelle ;

Yefanov, Andrey ;

Lee, Hyeseung ;

Zhang, Naigong ;

Robertson, Cynthia L. ;

Serova, Nadezhda ;

Davis, Sean ;

Soboleva, Alexandra .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D991-D995

[5]

Cooper L, 2016, METHODS MOL BIOL, V1374, P89, DOI 10.1007/978-1-4939-3167-5_5

[6] The Drosophila anatomy ontology [J].

Costa, Marta ;

Reeve, Simon ;

Grumbling, Gary ;

Osumi-Sutherland, David .

JOURNAL OF BIOMEDICAL SEMANTICS, 2013, 4

[7] The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability [J].

Diehl, Alexander D. ;

Meehan, Terrence F. ;

Bradford, Yvonne M. ;

Brush, Matthew H. ;

Dahdul, Wasila M. ;

Dougall, David S. ;

He, Yongqun ;

Osumi-Sutherland, David ;

Ruttenberg, Alan ;

Sarntivijai, Sirarat ;

Van Slyke, Ceri E. ;

Vasilevsky, Nicole A. ;

Haendel, Melissa A. ;

Blake, Judith A. ;

Mungall, Christopher J. .

JOURNAL OF BIOMEDICAL SEMANTICS, 2016, 7

[8] Guidelines for reporting single-cell RNA-seq experiments [J].

Fullgrabe, Anja ;

George, Nancy ;

Green, Matthew ;

Nejad, Parisa ;

Aronow, Bruce ;

Fexova, Silvie Korena ;

Fischer, Clay ;

Freeberg, Mallory Ann ;

Huerta, Laura ;

Morrison, Norman ;

Scheuermann, Richard H. ;

Taylor, Deanne ;

Vasilevsky, Nicole ;

Clarke, Laura ;

Gehlenborg, Nils ;

Kent, Jim ;

Marioni, John ;

Teichmann, Sarah ;

Brazma, Alvis ;

Papatheodorou, Irene .

NATURE BIOTECHNOLOGY, 2020, 38 (12) :1384-1386

[9] Bioconda: sustainable and comprehensive software distribution for the life sciences [J].

Gruening, Bjoern ;

Dale, Ryan ;

Sjoedin, Andreas ;

Chapman, Brad A. ;

Rowe, Jillian ;

Tomkins-Tinch, Christopher H. ;

Valieris, Renan ;

Koester, Johannes ;

Team, Bioconda .

NATURE METHODS, 2018, 15 (07) :475-476

[10]

Haendel M., 2009, Nature precedings, DOI 10.1038/npre.2009.3592.1

← 1 2 3 4 →