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Expression Atlas specifications

Information


Unique identifier OMICS_03311
Name Expression Atlas
Restrictions to use None
Data access File download, Browse
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Expression_Atlas

Publications for Expression Atlas

Expression Atlas citations

 (139)
library_books

Cross species inference of long non coding RNAs greatly expands the ruminant transcriptome

2018
PMCID: 5926538
PMID: 29690875
DOI: 10.1186/s12711-018-0391-0

[…] Previously, we created an expression atlas for the domestic sheep [], using both polyadenylated and rRNA-depleted RNA-seq data that were collected primarily from three male and three female adult Texel × Scottish Blackface (T  […]

library_books

Bioinformatics challenges and perspectives when studying the effect of epigenetic modifications on alternative splicing

2018
PMCID: 5915717
PMID: 29685977
DOI: 10.1098/rstb.2017.0073

[…] of experiments and outcomes from multiple sources. As a result, databases of experimental data and prior knowledge are required to maximize the data that can be analysed, such as ArrayExpress []. The Expression Atlas provides a map of gene expression over different tissues and cell types based on data in ArrayExpress [,]. Recently, the ISOexpresso database has been released that gives analogous in […]

library_books

Integrative bioinformatics analysis characterizing the role of EDC3 in mRNA decay and its association to intellectual disability

2018
BMC Med Genomics
PMCID: 5914069
PMID: 29685133
DOI: 10.1186/s12920-018-0358-6

[…] trols (Benjamini adjusted p-value < 0.1) (Additional file : Table S7). In order to assess whether the DEGs are preferentially expressed in neuronal cells, we utilized available expression data in the Expression Atlas []. Clustering of the expression of 744 DEGs listed in the Expression Atlas revealed a cluster of 117 genes, which are highly expressed in brain but rarely in other tissues (Fig. ; Ad […]

library_books

Genome wide identification of wheat (Triticum aestivum) expansins and expansin expression analysis in cold tolerant and cold sensitive wheat cultivars

2018
PLoS One
PMCID: 5875846
PMID: 29596529
DOI: 10.1371/journal.pone.0195138

[…] website (https://www.ncbi.nlm.nih.gov/unigene/). The sub-expression profile (measured as reads per kilobase of exon model per million mapped reads) was calculated from the E-MTAB-4484 datasets of the Expression Atlas (https://www.ebi.ac.uk/gxa/home) []. These datasets were generated using the Triticum aestivum cultivar Chinese Spring. All datasets are publicly available at the above two websites. […]

library_books

HLA and proteasome expression body map

2018
BMC Med Genomics
PMCID: 5872580
PMID: 29587858
DOI: 10.1186/s12920-018-0354-x

[…] mine the HLA type and expression of non-classical HLA class I molecules. Using the updated algorithm, we analyzed 4323 public RNA-Seq datasets to generate – to our knowledge - the first comprehensive expression atlas of HLA class I (classical and non -classical) and class II gene loci across 38 non-cancer tissues and 17 different cell types, including immune cell populations, pancreatic islets, pl […]

library_books

A group of nuclear factor Y transcription factors are sub functionalized during endosperm development in monocots

2018
J Exp Bot
PMCID: 5920288
PMID: 29514259
DOI: 10.1093/jxb/ery087

[…] Zm00001d017899 and Sb04g029340 were the most similar homologs of OsNF-YB1 in maize and sorghum, respectively (). By searching RNA-seq data deposited in the Expression Atlas database, we found that these genes are predominantly or exclusively expressed in endosperm (). Likewise, Zm00001d045772 (GRMZM2G167576) and Sb10g010520, the close homologs of OsNF-YB […]

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Expression Atlas institution(s)
European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK; Welcome Trust Sanger Institute, Hinxton, UK; Oregon State University, Corvallis, USA
Expression Atlas funding source(s)
European Molecular Biology Laboratory (EMBL) member states; National Science Foundation of USA grant to Gramene database [NSF IOS 1127112]; European Community's FP7 EurocanPlatform [260791]; BBSRC [BB/M018458/1]; CTTV; NHGRI, NHLBI; NIH Common Fund [U54-HG004028]; Wellcome Trust [WT098051]

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