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Expression Atlas: gene and protein expression across multiple studies and organisms

Irene Papatheodorou, Nuno A Fonseca, Maria Keays, Y Amy Tang, Elisabet Barrera, Wojciech Bazant, Melissa Burke, Anja Füllgrabe, Alfonso Muñoz-Pomer Fuentes, Nancy George, Laura Huerta, Satu Koskinen (+10 others)
2017 Nucleic Acids Research  
Expression Atlas (http://www.ebi.ac.uk/gxa) is an added value database that provides information about gene and protein expression in different species and contexts, such as tissue, developmental stage  ...  As of August 2017, Expression Atlas holds data from 3,126 studies across 33 different species, including 731 from plants.  ...  into ArrayExpress and European Nucleotide Archive; and our colleagues in Ensembl Genomes for the development of novel visualization of differential expression tracks from Atlas.  ... 
doi:10.1093/nar/gkx1158 pmid:29165655 pmcid:PMC5753389 fatcat:duqk25kctbauzihb22ieukvofa

Expression Atlas update: gene and protein expression in multiple species

Pablo Moreno, Silvie Fexova, Nancy George, Jonathan R Manning, Zhichiao Miao, Suhaib Mohammed, Alfonso Muñoz-Pomer, Anja Fullgrabe, Yalan Bi, Natassja Bush, Haider Iqbal, Upendra Kumbham (+22 others)
2021 Nucleic Acids Research  
(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.  ...  ACKNOWLEDGEMENTS We would like to thank Olamidipupo Ajigboye and Helen Parkinson for their contributions in enriching EFO in terms needed to describe samples studied in Atlas; Awais Athar, Ahmed Ali, Ugis  ... 
doi:10.1093/nar/gkab1030 pmid:34850121 pmcid:PMC8728300 fatcat:w4ochry6hreqhjcqkaezuperpe

PEATmoss (Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens

Noe Fernandez‐Pozo, Fabian B. Haas, Rabea Meyberg, Kristian K. Ullrich, Manuel Hiss, Pierre‐François Perroud, Sebastian Hanke, Viktor Kratz, Adrian F. Powell, Eleanor F. Vesty, Christopher G. Daum, Matthew Zane (+8 others)
2019 The Plant Journal  
Here, we introduce an interactive expression atlas, Physcomitrella Expression Atlas Tool (PEATmoss), that unifies publicly available expression data for P. patens and provides multiple visualization methods  ...  To facilitate gene expression queries across different gene annotation versions, and to access P. patens annotations and related resources, a lookup database and web tool linked to PEATmoss was implemented  ...  , Germany, through bwHPC and the German Research Foundation (DFG) through grant number INST 37/935-1 FUGG.  ... 
doi:10.1111/tpj.14607 pmid:31714620 fatcat:ua2ddy2ktjenbkmw4ulwlzv3e4

Expression Atlas update: from tissues to single cells

2019 Nucleic Acids Research  
Expression Atlas is EMBL-EBI's resource for gene and protein expression.  ...  Single Cell Expression Atlas was launched in 2018 and currently includes 123 single cell RNA-Seq studies from 12 species.  ...  ACKNOWLEDGEMENTS We would like to thank Olamidipupo Ajigboye and Helen Parkinson for their contributions in enriching EFO in terms needed to describe samples studied in Atlas; Awais Athar, Ahmed Ali, Ugis  ... 
doi:10.1093/nar/gkz947 pmid:31665515 pmcid:PMC7145605 fatcat:vp5gbm3mqbhjbhbucprqwyaggq

A human cell atlas of fetal gene expression

Junyue Cao, Diana R. O'Day, Hannah A. Pliner, Paul D. Kingsley, Mei Deng, Riza M. Daza, Michael A. Zager, Kimberly A. Aldinger, Ronnie Blecher-Gonen, Fan Zhang, Malte Spielmann, James Palis (+5 others)
2020 Science  
We generated human cell atlases of gene expression and chromatin accessibility in fetal tissues.  ...  We leveraged the literature and other atlases to identify and annotate hundreds of cell types and subtypes, both within and across tissues.  ...  For annotating cell typespecific gene features, we intersected the cell type-specific genes identified above with the predicted secreted and membrane protein coding gene sets from the Human Protein Atlas  ... 
doi:10.1126/science.aba7721 pmid:33184181 fatcat:rbbuaqq5jram3drf2fe5wf2pqy

A promoter-level mammalian expression atlas

2014 Nature  
gene expression across the human body.  ...  Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal.  ...  that share similar expression profiles across the atlas.  ... 
doi:10.1038/nature13182 pmid:24670764 pmcid:PMC4529748 fatcat:fkpyf4y6nbea5lq7v26lieaqlq

Gene Expression Atlas at the European Bioinformatics Institute

Misha Kapushesky, Ibrahim Emam, Ele Holloway, Pavel Kurnosov, Andrey Zorin, James Malone, Gabriella Rustici, Eleanor Williams, Helen Parkinson, Alvis Brazma
2009 Nucleic Acids Research  
The Gene Expression Atlas (http://www.ebi.ac .uk/gxa) is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states  ...  A simple interface allows the user to query for differential gene expression either (i) by gene names or attributes such as Gene Ontology terms, or (ii) by biological conditions, e.g. diseases, organism  ...  Sarkans on the gene reannotation pipeline; the work of Ugis Sarkans, Sergio Contrino and Hugo Berube on the earlier ArrayExpress Warehouse software served as a platform and motivation for the Atlas; Nikolay  ... 
doi:10.1093/nar/gkp936 pmid:19906730 pmcid:PMC2808905 fatcat:ruisihx4frgvbkwhmun2b6dyoy

The Medicago truncatula gene expression atlas web server

Ji He, Vagner A Benedito, Mingyi Wang, Jeremy D Murray, Patrick X Zhao, Yuhong Tang, Michael K Udvardi
2009 BMC Bioinformatics  
Flexible tools to select a subset of experiments and to visualize and compare expression profiles of multiple genes have been implemented.  ...  The web server will be updated on a regular basis to incorporate new gene expression data and genome annotation, and is accessible at: http://bioinfo.noble.org/gene-atlas/.  ...  genes/TCs), Foo Cheung, Christopher Town (JCVI; mapping probe sequences to the Medicago IMGAG v.  ... 
doi:10.1186/1471-2105-10-441 pmid:20028527 pmcid:PMC2804685 fatcat:rzmtgzumibdqnm4gp4o7uvbyfi

miRNA expression atlas in male rat

Keiichi Minami, Takeki Uehara, Yuji Morikawa, Ko Omura, Masayuki Kanki, Akira Horinouchi, Atsushi Ono, Hiroshi Yamada, Yasuo Ohno, Tetsuro Urushidani
2014 Scientific Data  
This work was supported in part by H14-001-Toxico and H19-001-Toxico grants from the Japanese Ministry of Health, Labour and Welfare.  ...  Institute of Biomedical Innovation (NIBIO), the National Institute of Health Science (NIHS) and several Japanese pharmaceutical companies.  ...  4 . 4 Expression profiles of organ-specific miRNAs identified in this study.  ... 
doi:10.1038/sdata.2014.5 pmid:25977763 pmcid:PMC4322570 fatcat:36kjqr6atfbyvk5eo2upnj2e3y

A gene expression atlas of the domestic pig

Tom C Freeman, Alasdair Ivens, J Kenneth Baillie, Dario Beraldi, Mark W Barnett, David Dorward, Alison Downing, Lynsey Fairbairn, Ronan Kapetanovic, Sobia Raza, Andru Tomoiu, Ramiro Alberio (+6 others)
2012 BMC Biology  
of an uncharacterized gene from the company it keeps and the locations in which it is expressed.  ...  In particular, we discuss the expression signatures associated with the gastrointestinal tract, an organ that was sampled at 15 sites along its length and whose biology in the pig is similar to human.  ...  We would also like to thank Dr Jane Loveland, The Sanger Institute, for her assistance in granting us access to the latest gene models available as part of the VEGA project and the team at Affymetrix,  ... 
doi:10.1186/1741-7007-10-90 pmid:23153189 pmcid:PMC3814290 fatcat:ktov6yler5bjtbxntnfnomlqbu

Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants

Robert Petryszak, Maria Keays, Y. Amy Tang, Nuno A. Fonseca, Elisabet Barrera, Tony Burdett, Anja Füllgrabe, Alfonso Muñoz-Pomer Fuentes, Simon Jupp, Satu Koskinen, Oliver Mannion, Laura Huerta (+12 others)
2015 Nucleic Acids Research  
Expression Atlas (http://www.ebi.ac.uk/gxa) provides information about gene and protein expression in animal and plant samples of different cell types, organism parts, developmental stages, diseases and  ...  Since the last update, Atlas has grown sevenfold (1572 studies as of August 2015), and incorporates baseline expression profiles of tissues from Human Protein Atlas, GTEx and FANTOM5, and of cancer cell  ...  of novel visualisation of differential expression tracks from Atlas.  ... 
doi:10.1093/nar/gkv1045 pmid:26481351 pmcid:PMC4702781 fatcat:ejfwhmtlcvbz3guoi6pkyacyji

SEAweb: the small RNA Expression Atlas web application

2019 Nucleic Acids Research  
We present the Small RNA Expression Atlas (SEAweb), a web application that allows for the interactive querying, visualization and analysis of known and novel small RNAs across 10 organisms.  ...  function and diagnostic value of sRNAs or pathogens across tissues, diseases and organisms.  ...  ACKNOWLEDGEMENTS We would like to thank Mariah Snyder, Yu Zhao, the ZMNH IT and all of the SEAweb users for helpful suggestions.  ... 
doi:10.1093/nar/gkz869 pmid:31598718 pmcid:PMC6943056 fatcat:s3adyrkmt5g2xp35rkn6pnmb2i

A Tissue-Specific Atlas of Mouse Protein Phosphorylation and Expression

Edward L. Huttlin, Mark P. Jedrychowski, Joshua E. Elias, Tapasree Goswami, Ramin Rad, Sean A. Beausoleil, Judit Villén, Wilhelm Haas, Mathew E. Sowa, Steven P. Gygi
2010 Cell  
Each tissue's unique physiology requires tightly regulated gene and protein expression coordinated by specialized, phosphorylation-dependent intracellular signaling.  ...  Although most tissues in an organism are genetically identical, the biochemistry of each is optimized to fulfill its unique physiological roles, with important consequences for human health and disease  ...  ACKNOWLEDGMENTS The authors thank Xue Li and Abir Mukherjee for help with phosphorylation studies and acknowledge Julian Mintseris, Deepak Kolippikam, Noah Dephoure, Younghao Yu, and other Gygi lab members  ... 
doi:10.1016/j.cell.2010.12.001 pmid:21183079 pmcid:PMC3035969 fatcat:sjkllsfvx5eclja7nnd4w6jnzi

Haemopedia: An Expression Atlas of Murine Hematopoietic Cells

Carolyn A. de Graaf, Jarny Choi, Tracey M. Baldwin, Jessica E. Bolden, Kirsten A. Fairfax, Aaron J. Robinson, Christine Biben, Clare Morgan, Kerry Ramsay, Ashley P. Ng, Maria Kauppi, Elizabeth A. Kruse (+17 others)
2016 Stem Cell Reports  
Here we present Haemopedia, an atlas of murine gene-expression data containing 54 hematopoietic cell types, covering all the mature lineages in hematopoiesis.  ...  This resource provides simple tools to interrogate gene-expression-based relationships between hematopoietic cell types and genes of interest.  ...  ACKNOWLEDGMENTS The authors would like to thank the many people who contributed to this project, with numerous feedback and involvement.  ... 
doi:10.1016/j.stemcr.2016.07.007 pmid:27499199 pmcid:PMC5031953 fatcat:wnkzzlegf5fmxd3jnayb3unjmy

EMAGE—Edinburgh Mouse Atlas of Gene Expression: 2008 update

Shanmugasundaram Venkataraman, Peter Stevenson, Yiya Yang, Lorna Richardson, Nicholas Burton, Thomas P. Perry, Paul Smith, Richard A. Baldock, Duncan R. Davidson, Jeffrey H. Christiansen
2007 Nucleic Acids Research  
subsequent hierarchical-clustering, and spatial searches across multiple stages of development.  ...  EMAGE (http://genex.hgu.mrc.ac.uk/Emage/data base) is a database of in situ gene expression patterns in the developing mouse embryo.  ...  yield image-based information about spatially complex patterns of gene expression within tissues and organisms.  ... 
doi:10.1093/nar/gkm938 pmid:18077470 pmcid:PMC2238921 fatcat:6mh6ip3s7bfdhl5ir5yhnypkae
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