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Expression Atlas update: from tissues to single cells

2019 Nucleic Acids Research  
Single Cell Expression Atlas was launched in 2018 and currently includes 123 single cell RNA-Seq studies from 12 species.  ...  With the increased availability of single cell RNA-Seq datasets in the public archives, we have now extended Expression Atlas with a new added-value service to display gene expression in single cells.  ...  We would like to thank our collaborators from  ... 
doi:10.1093/nar/gkz947 pmid:31665515 pmcid:PMC7145605 fatcat:vp5gbm3mqbhjbhbucprqwyaggq

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  
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  ...  Expression Atlas is currently divided into Bulk Expression Atlas and Single Cell Expression Atlas.  ...  We would like to thank the data wranglers of the Human Cell Atlas Data Coordination Platform for their assistance collating HCA data for the Single Cell Expression Atlas.  ... 
doi:10.1093/nar/gkab1030 pmid:34850121 pmcid:PMC8728300 fatcat:w4ochry6hreqhjcqkaezuperpe

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  
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  ...  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  ...  of novel visualisation of differential expression tracks from Atlas.  ... 
doi:10.1093/nar/gkv1045 pmid:26481351 pmcid:PMC4702781 fatcat:ejfwhmtlcvbz3guoi6pkyacyji

Ex uno, plures–From One Tissue to Many Cells: A Review of Single-Cell Transcriptomics in Cardiovascular Biology

Elvira Forte, Micheal A. McLellan, Daniel A. Skelly, Nadia A. Rosenthal
2021 International Journal of Molecular Sciences  
Single-cell profiling provides a more precise definition of tissue composition, cell differentiation trajectories, and intercellular communication, compared to classical bulk approaches.  ...  Here, we aim to review how recent single-cell multi-omic studies have changed our understanding of cell dynamics during cardiac development, and in the healthy and diseased adult myocardium.  ...  ECs from CTR and -V-VEGF-B transduced adult hearts Cardiac scRNAseq Cell Atlases Single-cell transcriptomic analysis deepens our understanding of tissue complexity as well as the dynamic nature of tissue  ... 
doi:10.3390/ijms22042071 pmid:33669808 fatcat:muekv4dz3vhkdcotraipsq2j2e

Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

Robert Petryszak, Tony Burdett, Benedetto Fiorelli, Nuno A. Fonseca, Mar Gonzalez-Porta, Emma Hastings, Wolfgang Huber, Simon Jupp, Maria Keays, Nataliya Kryvych, Julie McMurry, John C. Marioni (+9 others)
2013 Nucleic Acids Research  
successor, Expression Atlas.  ...  Finally, they would like to thank Misha Kapushesky and other previous developers of Gene Expression Atlas for their work and input, which will have inevitably influenced our efforts when developing its  ...  remit as a value-added database for querying differential gene expression across tissues, cell types and cell lines under various biological conditions.  ... 
doi:10.1093/nar/gkt1270 pmid:24304889 pmcid:PMC3964963 fatcat:bl7yghza35e55ivxrk7ojfnx5q

SEA: The Small RNA Expression Atlas [article]

Raza-Ur Rahman, Abdul Sattar, Maksims Fiosins, Abhivyakti Gautam, Daniel Sumner Magruder, Joern Bethune, Sumit Madan, Juliane Fluck, Stefan Bonn
2017 bioRxiv   pre-print
across samples, organisms, tissues, cell types, and diseases.  ...  Motivation: Small RNAs (sRNAs) are important biomolecules that exert vital functions in organismal health and disease, from viruses to plants, animals, and humans.  ...  ACKNOWLEDGEMENTS We would like to thank Mariah Snyder, Ashish Rajput, Ting Sun, Vikas Bansal, Michel Edwar Mickael, the DZNE IT, and all of the Oasis users for helpful suggestions.  ... 
doi:10.1101/133199 fatcat:o2q67o6dcfgarlr4j4gswkkbqm

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  
As of August 2017, Expression Atlas holds data from 3,126 studies across 33 different species, including 731 from plants.  ...  In addition to the web interface, data sets can now be searched and downloaded through the Expression Atlas R package.  ...  We would also like to extend our thanks to our colleagues in WormBase and Complex Portal for incorporating Atlas tissue expression widget in their resources.  ... 
doi:10.1093/nar/gkx1158 pmid:29165655 pmcid:PMC5753389 fatcat:duqk25kctbauzihb22ieukvofa

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments

M. Kapushesky, T. Adamusiak, T. Burdett, A. Culhane, A. Farne, A. Filippov, E. Holloway, A. Klebanov, N. Kryvych, N. Kurbatova, P. Kurnosov, J. Malone (+10 others)
2011 Nucleic Acids Research  
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, sample  ...  A simple interface allows the user to query  ...  ACKNOWLEDGEMENTS In addition to the invaluable help from the entire Functional Genomics Team, led by Ugis Sarkans, we would like to thank particularly Ekaterina Pilicheva for help with gene re-annotation  ... 
doi:10.1093/nar/gkr913 pmid:22064864 pmcid:PMC3245177 fatcat:qi4tj2jmszh3zdkwmbwotggyo4

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  
to query the data in a single web-based tool.  ...  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  ...  Figures can represent the expression of one single tissue or can be formed by combination of several drawings to display the expression of multiple tissues in one single image.  ... 
doi:10.1111/tpj.14607 pmid:31714620 fatcat:ua2ddy2ktjenbkmw4ulwlzv3e4

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.  ...  For gene expression, we applied three-level combinatorial indexing to >110 samples representing 15 organs, ultimately profiling ~4 million single cells.  ...  As one step toward a comprehensive cell atlas of human development (10) , we set out to generate single-cell atlases of both gene expression and chromatin accessibility using diverse human tissues obtained  ... 
doi:10.1126/science.aba7721 pmid:33184181 fatcat:rbbuaqq5jram3drf2fe5wf2pqy

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.  ...  SEAweb's user model enables sRNA researchers to compare and re-analyze user-specific and published datasets, highlighting common and distinct sRNA expression patterns.  ...  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

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  
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/.  ...  With the rapid growth of publically available Affymetrix GeneChip Medicago Genome Array GeneChip data from a great range of tissues, cell types, growth conditions, and stress treatments, the legume research  ...  Acknowledgements We would like to thank the following colleagues for sharing their published data and for assisting our data curation: Haiquan Li, Xinbin Dai (updated mapping between probesets and Medicago  ... 
doi:10.1186/1471-2105-10-441 pmid:20028527 pmcid:PMC2804685 fatcat:rzmtgzumibdqnm4gp4o7uvbyfi

Gateways to the FANTOM5 promoter level mammalian expression atlas

Marina Lizio, Jayson Harshbarger, Hisashi Shimoji, Jessica Severin, Takeya Kasukawa, Serkan Sahin, Imad Abugessaisa, Shiro Fukuda, Fumi Hori, Sachi Ishikawa-Kato, Christopher J Mungall, Erik Arner (+29 others)
2015 Genome Biology  
The FANTOM5 project investigates transcription initiation activities in more than 1,000 human and mouse primary cells, cell lines and tissues using CAGE.  ...  the FANTOM5 atlas.  ...  Acknowledgements Figure 1 are provided by Gundula G Schulze-Tanzil (tenocyte), Anna Ehrlund (Adipocyte), RIKEN BRC (cell lines), and BodyParts 3D (tissues).  ... 
doi:10.1186/s13059-014-0560-6 pmid:25723102 pmcid:PMC4310165 fatcat:7p63sfdvszgc7oetvsyomnr2v4

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  ...  The gene queries return the conditions where expression has been reported, while condition queries return which genes are reported to be expressed in these conditions.  ...  ACKNOWLEDGEMENTS In addition to the invaluable help from the entire Microarrays Team, we would like to thank especially the work of Richard Coulson, Ekaterina Pilicheva, Niran Abeygunawardena and Ugis  ... 
doi:10.1093/nar/gkp936 pmid:19906730 pmcid:PMC2808905 fatcat:ruisihx4frgvbkwhmun2b6dyoy

HPAStainR: a Bioconductor and Shiny app to query protein expression patterns in the Human Protein Atlas

Tim O. Nieuwenhuis, Marc K. Halushka
2021 F1000Research  
The Human Protein Atlas is a website of protein expression in human tissues.  ...  It is an excellent resource of tissue and cell type protein localization, but only allows the query of a single protein at a time.  ...  Therefore, across both single cell and bulk gene expression data, we have identified useful functionality to HPAStainR.  ... 
doi:10.12688/f1000research.26771.2 fatcat:bhbefnnhnvbm7osqnlsvad2yde
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