Comparison of the transcriptional landscapes between human and mouse tissues

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 48, 2014, Pages 17224-17229

  Lin, Shin ^a,b   Lin, Yiing ^c   Nery, Joseph R ^d   Urich, Mark A ^d   Breschi, Alessra ^e,f   Davis, Carrie A ^g   Dobin, Alexer ^g   Zaleski, Christopher ^g   Beer, Michael A ^h   Chapman, William C ^c   Gingeras, Thomas R ^g,i   Ecker, Joseph R ^d,j   Snyder, Michael P ^a  

^a STANFORD UNIVERSITY   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d SALK INSTITUTE FOR BIOLOGICAL STUDIES   (United States)

^e CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^f UNIVERSITAT POMPEU FABRA   (Spain)

^g Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^h Johns Hopkins University   (United States)

ⁱ Thermo Fisher Scientific   (United States)

^j HOWARD HUGHES MEDICAL INSTITUTE   (United States)

more..

Author keywords

Epigenome; Noncoding transcripts; Species comparison; Transcriptome

Indexed keywords

MUS;

PROTEIN; SPACER DNA; TRANSCRIPTOME;

ANIMAL; ANTIBODY SPECIFICITY; C57BL MOUSE; COMPARATIVE STUDY; EPIGENETICS; GENE EXPRESSION PROFILING; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; MOLECULAR EVOLUTION; PROCEDURES; SEQUENCE ANALYSIS; SPECIES DIFFERENCE;

ANIMALS; DNA, INTERGENIC; EPIGENOMICS; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICE, INBRED C57BL; ORGAN SPECIFICITY; PROTEINS; SEQUENCE ANALYSIS, RNA; SPECIES SPECIFICITY; TRANSCRIPTOME;

EID: 84914125316     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1413624111     Document Type: Article

References (25)

1. Barbosa-Morais NL, et al. (2012) The evolutionary landscape of alternative splicing in vertebrate species. Science 338(6114):1587-1593.
2. Merkin J, Russell C, Chen P, Burge CB (2012) Evolutionary dynamics of gene and isoform regulation in Mammalian tissues. Science 338(6114):1593-1599.
3. Bernstein BE, et al. (2010) The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol 28(10):1045-1048.
4. Lonsdale J, et al.; GTEx Consortium (2013) The Genotype-Tissue Expression (GTEx) project. Nat Genet 45(6):580-585.
5. Brawand D, et al. (2011) The evolution of gene expression levels in mammalian organs. Nature 478(7369):343-348.
6. Schug J, et al. (2005) Promoter features related to tissue specificity as measured by Shannon entropy. Genome Biol 6(4):R33.
7. Ashburner M, et al.; The Gene Ontology Consortium (2000) Gene ontology: Tool for the unification of biology. Nat Genet 25(1):25-29.
8. Dunham I, et al.; ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57-74.
9. Dong X, et al. (2012) Modeling gene expression using chromatin features in various cellular contexts. Genome Biol 13(9):R53.
10. Wang Z, et al. (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40(7):897-903.
11. Zhu J, et al. (2013) Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell 152(3):642-654.
12. Kim TK, et al. (2010) Widespread transcription at neuronal activity-regulated enhancers. Nature 465(7295):182-187.
13. Cabili MN, et al. (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25(18):1915-1927.
14. Harrow J, et al. (2012) GENCODE: The reference human genome annotation for The ENCODE Project. Genome Res 22(9):1760-1774.
15. Washietl S, Kellis M, Garber M (2014) Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals. Genome Res 24(4):616-628.
16. Guttman M, et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458(7235):223-227.
17. Derrien T, et al. (2012) The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res 22(9):1775-1789.
18. Church DM, et al.; Mouse Genome Sequencing Consortium (2009) Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol 7(5):e1000112.
19. Hinrichs AS, et al. (2006) The UCSC Genome Browser Database: Update 2006. Nucleic Acids Res 34(Database issue):D590-D598.
20. Papasaikas P, Valcárcel J (2012) Evolution. Splicing in 4D. Science 338(6114): 1547-1548.
21. Seok J, et al.; Inflammation and Host Response to Injury, Large Scale Collaborative Research Program (2013) Genomic responses in mouse models poorly mimic human inflammatory diseases. Proc Natl Acad Sci USA 110(9):3507-3512.
22. Borneman AR, et al. (2007) Divergence of transcription factor binding sites across related yeast species. Science 317(5839):815-819.
23. Cheng Y, et al. (2014) Principles of regulatory information conservation revealed by comparing mouse and human transcription factor binding profiles. Nature, in press.
24. Trapnell C, et al. (2012) Differential gene and transcript expression analysis of RNAseq experiments with TopHat and Cufflinks. Nat Protoc 7(3):562-578.
25. Wang L, et al. (2013) CPAT: Coding-Potential Assessment Tool using an alignmentfree logistic regression model. Nucleic Acids Res 41(6):e74.