Global regulatory architecture of human, mouse and rat tissue transcriptomes.

Details

Serval ID
serval:BIB_D8F8780B6342
Type
Article: article from journal or magazin.
Collection
Publications
Title
Global regulatory architecture of human, mouse and rat tissue transcriptomes.
Journal
BMC genomics
Author(s)
Prasad A., Kumar S.S., Dessimoz C., Bleuler S., Laule O., Hruz T., Gruissem W., Zimmermann P.
ISSN
1471-2164 (Electronic)
ISSN-L
1471-2164
Publication state
Published
Issued date
20/10/2013
Peer-reviewed
Oui
Volume
14
Pages
716
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: epublish
Abstract
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.
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.
The results demonstrate that tissue-specific regulation is the main determinant of transcriptome composition and is highly conserved across mammalian species.
Keywords
Animals, Cluster Analysis, Genome, Genome, Human, Humans, Mice, Multigene Family, Oligonucleotide Array Sequence Analysis, Principal Component Analysis, Rats, Species Specificity, Transcriptome
Pubmed
Web of science
Open Access
Yes
Create date
02/09/2015 8:16
Last modification date
06/03/2024 10:34
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