Global regulatory architecture of human, mouse and rat tissue transcriptomes View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2013-12

AUTHORS

Ajay Prasad, Suchitra Suresh Kumar, Christophe Dessimoz, Stefan Bleuler, Oliver Laule, Tomas Hruz, Wilhelm Gruissem, Philip Zimmermann

ABSTRACT

BACKGROUND: Predicting molecular responses in human by extrapolating results from model organisms requires a precise understanding of the architecture and regulation of biological mechanisms across species. RESULTS: Here, we present a large-scale comparative analysis of organ and tissue transcriptomes involving the three mammalian species human, mouse and rat. To this end, we created a unique, highly standardized compendium of tissue expression. Representative tissue specific datasets were aggregated from more than 33,900 Affymetrix expression microarrays. For each organism, we created two expression datasets covering over 55 distinct tissue types with curated data from two independent microarray platforms. Principal component analysis (PCA) revealed that the tissue-specific architecture of transcriptomes is highly conserved between human, mouse and rat. Moreover, tissues with related biological function clustered tightly together, even if the underlying data originated from different labs and experimental settings. Overall, the expression variance caused by tissue type was approximately 10 times higher than the variance caused by perturbations or diseases, except for a subset of cancers and chemicals. Pairs of gene orthologs exhibited higher expression correlation between mouse and rat than with human. Finally, we show evidence that tissue expression profiles, if combined with sequence similarity, can improve the correct assignment of functionally related homologs across species. CONCLUSION: The results demonstrate that tissue-specific regulation is the main determinant of transcriptome composition and is highly conserved across mammalian species. More... »

PAGES

716

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2164-14-716

DOI

http://dx.doi.org/10.1186/1471-2164-14-716

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1027575431

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/24138449


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curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-14-716'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-14-716'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-14-716'


 

This table displays all metadata directly associated to this object as RDF triples.

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