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RNA-Seq Atlas specifications


Unique identifier OMICS_10922
Name RNA-Seq Atlas
Restrictions to use None
Data access File download, Browse
Maintained Yes


  • Primates
    • Homo sapiens

Publication for RNA-Seq Atlas

RNA-Seq Atlas citations


Computational de novo discovery of distinguishing genes for biological processes and cell types in complex tissues

PLoS One
PMCID: 5832224
PMID: 29494600
DOI: 10.1371/journal.pone.0193067

[…] t these high error rates, the cell type signatures were relatively faithful to the expected signatures, especially for the more distinct cell types. For the multi-tissue simulated data set built from RNA-seq Atlas data, the worst RMSE for a uniform distribution mixture would be 0.14. Predictions with RMSE values above this level can be considered worse than random. CellDistinguisher coupled with s […]


Hypoxia tolerance, longevity and cancer resistance in the mole rat Spalax – a liver transcriptomics approach

Sci Rep
PMCID: 5662568
PMID: 29084988
DOI: 10.1038/s41598-017-13905-z

[…] To compare expression differences between Spalax and rat in genes known to be differentially expressed in liver cancer, we created two sets of genes using the RNA Seq Atlas resource (http://medicalgenomics.org/rna_seq_atlas ). The first list consisted of 32 genes consistently upregulated in 15 different liver cancer cell lines, representing candidate oncoge […]


Pea Marker Database (PMD) – A new online database combining known pea (Pisum sativum L.) gene based markers

PLoS One
PMCID: 5658071
PMID: 29073280
DOI: 10.1371/journal.pone.0186713

[…] available in MtGEA was found for 61% of the sequences.The functional annotation of markers from the ACm set includes information about the expression profile of the corresponding transcript from Pea RNA-seq Atlas available online at http://bios.dijon.inra.fr/FATAL/cgi/pscam.cgi [].Visualization of the database content was conducted using D3.js, a JavaScript library for manipulating documents base […]


Translocational renal cell carcinoma (t(6;11)(p21;q12) with transcription factor EB (TFEB) amplification and an integrated precision approach: a case report

PMCID: 4674949
PMID: 26654961
DOI: 10.1186/s13256-015-0749-7

[…] M) expression (Table ).A plot of normalized transcript counts is shown in Fig. . In order to estimate upregulation of transcription compared to a normal kidney, we obtained transcript counts from the RNA-Seq Atlas [] (Fig. ). In order to evaluate whether there was an expression effect of TFEB being overexpressed, we examined whether genes that previously had been reported as upregulated in transie […]


Genome wide analysis and expression profiling under heat and drought treatments of HSP70 gene family in soybean (Glycine max L.)

Front Plant Sci
PMCID: 4585176
PMID: 26442082
DOI: 10.3389/fpls.2015.00773

[…] To acquire the tissue-specific transcript data, the 61 GmHSP70 genes were investigated based on the RNA Seq-Atlas from fourteen tissues (http://soybase.org/soyseq/), including underground tissues (root and nodule), seed development (seed 10-DAF, seed 14-DAF, seed 21-DAF, seed 25-DAF, seed 28-DAF, se […]


Genome wide annotation and characterization of CLAVATA/ESR (CLE) peptide hormones of soybean (Glycine max) and common bean (Phaseolus vulgaris), and their orthologues of Arabidopsis thaliana

J Exp Bot
PMCID: 4526924
PMID: 26188205
DOI: 10.1093/jxb/erv351
call_split See protocol

[…] Transcriptional data for the meta-analysis was collected from publicly available data sets from the Soybean RNA-Seq Atlas (http://www.soybase.org/soyseq/; ); the Soybean eFP Browser (http://bar.utoronto.ca/efpsoybean/cgi-bin/efpWeb.cgi; ); A Common Bean Gene Expression Atlas (http://plantgrn.noble.org/PvGEA […]


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RNA-Seq Atlas institution(s)
Department of Medicine I, Johannes Gutenberg University, Mainz, Germany; Translational Oncology and Immunology (TRON), Johannes Gutenberg University, Mainz, Germany
RNA-Seq Atlas funding source(s)
This study was supported by a research grant of the Boehringer Ingelheim Foundation and funding of the core facility bioinformatics of the University Hospital of the Johannes Gutenberg University Mainz, Germany.

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