Global regulatory architecture of human, mouse and rat tissue transcriptomes

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Prasad, Ajay ^a   Kumar, Suchitra S ^a   Dessimoz, Christophe ^a,c,d   Bleuler, Stefan ^b   Laule, Oliver ^b   Hruz, Tomas ^a,b   Gruissem, Wilhelm ^a   Zimmermann, Philip ^a,b  

^a ETH ZURICH   (Switzerland)

^b NEBION AG   (Switzerland)

^c SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^d UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL COMPOUND; TRANSCRIPTOME;

ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; GENE EXPRESSION PROFILING; GENETIC CONSERVATION; GENETIC DATABASE; GENETIC REGULATION; HUMAN; MICROARRAY ANALYSIS; MOUSE; NEOPLASM; NONHUMAN; ORGAN; ORTHOLOGY; RAT; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; STANDARDIZATION; STRUCTURE ANALYSIS; TISSUE SPECIFICITY; TISSUE STRUCTURE; ANIMAL; CLUSTER ANALYSIS; DNA MICROARRAY; GENOME; HUMAN GENOME; MULTIGENE FAMILY; PRINCIPAL COMPONENT ANALYSIS;

MAMMALIA; RATTUS;

ANIMALS; CLUSTER ANALYSIS; GENOME; GENOME, HUMAN; HUMANS; MICE; MULTIGENE FAMILY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PRINCIPAL COMPONENT ANALYSIS; RATS; SPECIES SPECIFICITY; TRANSCRIPTOME;

EID: 84885560067     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-716     Document Type: Article

References (39)

1. Bennett CN, Green JE. Unlocking the power of cross-species genomic analyses: identification of evolutionarily conserved breast cancer networks and validation of preclinical models. Breast Cancer Res 2008, 10:213. 10.1186/bcr2125, 2614501, 18828875.
2. Wartman LD, Larson DE, Xiang Z, Ding L, Chen K, Lin L, Cahan P, Klco JM, Welch JS, Li C, Payton JE, Uy GL, Varghese N, Ries RE, Hoock M, Koboldt DC, McLellan MD, Schmidt H, Fulton RS, Abbott RM, Cook L, McGrath SD, Fan X, Dukes AF, Vickery T, Kalicki J, Lamprecht TL, Graubert TA, Tomasson MH, Mardis ER, et al. Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression. J Clin Invest 2011, 121(4):1445-1455. 10.1172/JCI45284, 10.1172/JCI45284, 3069786, 21436584.
3. Yanai I, Graur D, Ophir R. Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control. Omics : J Integr Biol 2004, 8:15-24.
4. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 2004, 101(16):6062-6067. 10.1073/pnas.0400782101, 395923, 15075390.
5. Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega RG, Sapinoso LM, Moqrich A, Patapoutian A, Hampton GM, Schultz PG, Hogenesch JB. Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A 2002, 99(7):4465-4470. 10.1073/pnas.012025199, 123671, 11904358.
6. Zheng-Bradley X, Rung J, Parkinson H, Brazma A. Large scale comparison of global gene expression patterns in human and mouse. Genome Biol 2010, 11:R124. 10.1186/gb-2010-11-12-r124, 3046484, 21182765.
7. Liao BY, Zhang J. Evolutionary conservation of expression profiles between human and mouse orthologous genes. Mol Biol Evol 2006, 23(3):530-540.
8. Bergmann S, Ihmels J, Barkai N. Similarities and differences in genome-wide expression data of six organisms. PLoS Biol 2003, 2:e9. 300882, 14737187.
9. Rustici G, Mata J, Kivinen K, Lio P, Penkett C, Burns G, Hayles J, Brazma A, Nurse P, Bahler J. Periodic gene expression program of the fission yeast cell cycle. Nat Genet 2004, 36(5):809-17.
10. Han ES, Hickey M. Microarray evaluation of dietary restriction. J Nutr 2005, 135(6):1343-1346.
11. Yanai I, Korbel JO, Boue S, McWeeney SK, Bork P, Lercher MJ. Similar gene expression profiles do not imply similar tissue functions. Trends Genet 2006, 22(3):132-138. 10.1016/j.tig.2006.01.006, 16480787.
12. Lelandais G, Crom S. Cross-Species Comparison Using Expression Data. Introduction to Systems Biology 2007, 147-159: Humana Press, Choi S, doi:10.1007/978-1-59745-531-2-8.
13. Fang H, Tong W, Perkins R, Shi L, Hong H, Cao X, Xie Q, Yim S, Ward J, Pitot H, Dragan Y. Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling. BMC bioinformatics 2005, 6(Suppl 2):S6.
14. Liao BY, Zhang J. Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution. Mol Biol Evol 2006, 23(6):1119-1128. 10.1093/molbev/msj119, 16520335.
15. Chen J, Blackwell TW, Fermin D, Menon R, Chen Y, Gao J, Lee AW, State DJ. Evolutionary-conserved gene expression response profiles across mammalian tissues. OMICS: J Integr Biol 2007, 11:96-122.
16. Chan E, Quon G, Chua G, Babak T, Trochesset M, Zirngibl R, Aubin J, Ratcliffe M, Wilde A, Brudno M, Morris Q, Hughes T. Conservation of core gene expression in vertebrate tissues. J Biol 2009, 8(3):33. 10.1186/jbiol130, 2689434, 19371447.
17. Brawand D, Soumillon M, Necsulea A, Julien P, Csárdi G, Harrigan P, Weier M, Liechti A, Aximu-Petri A, Kircher M, Albert FW, Zeller U, Khaitovich P, Grützner F, Bergmann S, Nielsen R, Paabo S, Kaessmann H. The evolution of gene expression levels in mammalian organs. Nature 2011, 478(7369):343-348. 10.1038/nature10532, 22012392.
18. Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W, Zimmermann P. Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Adv Bioinformatics 2008, 2008:420747. 2777001, 19956698.
19. Schneider A, Dessimoz C, Gonnet GH. OMA Browser-exploring orthologous relations across 352 complete genomes. Bioinformatics 2007, 23:2180-2182. 10.1093/bioinformatics/btm295, 17545180.
20. Lukk M, Kapushesky M, Nikkila J, Parkinson H, Goncalves A, Huber W, Ukkonen E, Brazma A. A global map of human gene expression. Nat Biotechnol 2010, 28(4):322-324. 10.1038/nbt0410-322, 2974261, 20379172.
21. Somel M, Creely H, Franz H, Mueller U, Lachmann M, Khaitovich P, Paabo S. Human and chimpanzee gene expression differences replicated in mice fed different diets. PLoS ONE 2008, 3:e1504. 10.1371/journal.pone.0001504, 2200793, 18231591.
22. Birgersdotter A, Sandberg R, Ernberg I. Gene expression perturbation in vitro-a growing case for three-dimensional (3D) culture systems. Semin Cancer Biol 2005, 15(5):405-412. 10.1016/j.semcancer.2005.06.009, 16055341.
23. Sandberg R, Ernberg I. The molecular portrait of in vitro growth by meta-analysis of gene-expression profiles. Genome Biol 2005, 6(8):R65. 10.1186/gb-2005-6-8-r65, 1273632, 16086847.
24. Underhill GH, Galie P, Chen CS, Bhatia SN. Bioengineering methods for analysis of cells in vitro. Annu Rev Cell Dev Biol 2012, 28:385-410. 10.1146/annurev-cellbio-101011-155709, 23057744.
25. Liu JS, Gartner ZJ. Directing the assembly of spatially organized multicomponent tissues from the bottom up. Trends Cell Biol 2012, 22(12):683-691. 10.1016/j.tcb.2012.09.004, 23067679.
26. Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5:101-113. 10.1038/nrg1272, 14735121.
27. Fitch W. Distinguishing homologous from analogous proteins. Syst Zool 1970, 19(2):99-113. 10.2307/2412448, 5449325.
28. Studer RA, Robinson-Rechavi M. How confident can we be that orthologs are similar, but paralogs differ?. Trends Genet : TIG 2009, 25(5):210-216.
29. Koonin EV. Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet 2005, 39:309-338. 10.1146/annurev.genet.39.073003.114725, 16285863.
30. Huminiecki L, Wolfe KH. Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse. Genome Res 2004, 14:1870-1879. 10.1101/gr.2705204, 524410, 15466287.
31. Li WH, Yang J, Gu X. Expression divergence between duplicate genes. Trends Genet 2005, 21:602-607. 10.1016/j.tig.2005.08.006, 16140417.
32. Makova KD, Li WH. Divergence in the spatial pattern of gene expression between human duplicate genes. Genome Res 2003, 13:1638-1645. 10.1101/gr.1133803, 403737, 12840042.
33. Altenhoff AM, Studer RA, Robinson-Rechavi M, Dessimoz C. Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs. PLOS Comput Biol 2012, 8(5):e1002514. 10.1371/journal.pcbi.1002514, 3355068, 22615551.
34. Blanc G, Wolfe KH. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 2004, 16:1679-1691. 10.1105/tpc.021410, 514153, 15208398.
35. Dowell R. The similarity of gene expression between human and mouse tissues. Genome Biol 2011, 12:101. 10.1186/gb-2011-12-1-101, 3091293, 21241524.
36. Altenhoff AM, Schneider A, Gonnet GH, Dessimoz C. OMA 2011: orthology inference among 1000 complete genomes. Nucleic Acids Res 2011, 39(Database issue):D289-D294. 3013747, 21113020.
37. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003, 31(4):e15. 10.1093/nar/gng015, 150247, 12582260.
38. Zheng Q, Wang XJ. GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res 2008, 36(Web Server issue):W358-W363. 2447756, 18487275.
39. Jantzen SG, Sutherland BJ, Minkley DR, Koop BF. GO Trimming: Systematically reducing redundancy in large Gene Ontology datasets. BMC Res Notes 2011, 4:267. 10.1186/1756-0500-4-267, 3160396, 21798041.