Cross species analysis of microarray expression data

Bioinformatics

Volumn 25, Issue 12, 2009, Pages 1476-1483

  Lu, Yong ^a,b   Huggins, Peter ^a   Bar Joseph, Ziv ^a  

^a Carnegie Mellon University   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY; COMPUTER ANALYSIS; DATA ANALYSIS; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENETIC CONSERVATION; HUMAN; MICROARRAY ANALYSIS; NONHUMAN; PRIORITY JOURNAL; REVIEW; SEQUENCE ANALYSIS; SPECIES COMPARISON;

ANIMALS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SPECIES SPECIFICITY;

EID: 66349116028     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp247     Document Type: Review

References (65)

1. Alexander,P.A. et al. (2007) The design and characterization of two proteins with 88% sequence identity but different structure and function. Proc. Natl Acad. Sci. USA, 104, 11963-11968.
2. Alter,O. et al. (2003) Generalized singular value decomposition for comparative analysis of genome-scale expression datasets of two different organisms. Proc. Natl Acad. Sci. USA, 100, 3351-3356.
3. Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
4. Arbeitman,M.N. et al. (2002) Gene expression during the life cycle of Drosophila melanogaster. Science, 298, 2270-2275.
5. Bergmann,S. et al. (2004) Similarities and differences in genome-wide expression data of six organisms. PLoS Biol., 2, 86-93.
6. Bigger,C.B. et al. (2001) DNA microarray analysis of chimpanzee liver during acute resolving hepatitis C virus infection. J. Virol. 75, 7059-7066.
7. Cahan,P. et al. (2005) List of lists-annotated (LOLA): A database for annotation and comparison of published microarray gene lists. Gene, 360, 78-82.
8. Choi,J. et al. (2003) Combining multiple microarray studies and modeling interstudy variation. Bioinformatics, 19, 84-90.
9. Correa,A. et al. (2003) Multiple oscillators regulate circadian gene expression in Neurospora. Proc. Natl Acad. Sci. USA, 100 13597-13602.
10. Durbin,R. et al. (1998) Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, UK.
11. Dyczkowski,J. and Vingron,M. (2005) Comparative analysis of cell cycle regulated genes in eukaryotes. Genome Informatics, 16, 125-131.
12. Fortunel,N.O. et al. (2003) Comment on "Stemness: Transcriptional profiling of embryonic and adult stem cells" and "A stem cells molecular signature". Science, 302, 393.
13. Gilad,Y. et al. (2005) Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res., 15, 674-680.
14. Gilad,Y. et al. (2006) Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature, 440, 242-245.
15. Han,E. and Hickey,M. (2005) Microarray evaluation of dietary restriction. J. Nutr., 135, 1343-1346.
16. Harbison,C.T. et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99-104.
17. Hong,F. and Breitling,R. (2008) A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments. Bioinformatics, 24, 374-382.
18. Huang,D.W. et al. (2009) Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nat. Protoc. 4, 44-57.
19. Irizarry,R.A. et al. (2005) Multiple-laboratory comparison of microarray platforms. Nat. Methods, 2, 345-350.
20. Jensen,L.J. et al. (2006) Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature, 443, 594-597.
21. Jensen,L.J. et al. (2008). Circular reasoning rather than cyclic expression. Genome Biol., 9, 403.
22. Kamvysselis,M. et al. (2003) Whole-genome comparative annotation and regulatory motif discovery in multiple yeast species. In Proceedings of the Seventh International Conference on Research in Computational Molecular Biology, ACM Press, New York, NY, USA, pp. 157-166.
23. Kellis,M. et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature, 423, 241-254.
24. Khaitovich,P. et al. (2005) Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science, 309, 1850-1854.
25. Kirst,M. et al. (2006) Genetic diversity contribution to errors in short oligonucleotide microarray analysis. Plant Biotechnol. J., 4, 489-498.
26. Krogan,N.J. et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature, 440, 637-643.
27. Kumar,A. et al. (2005) Abstracting genes to gene ontology terms allows comparison across multiple species. In Proceedings of the 18th International Conference on Systems Engineering, IEEE Computer Society Press, Los Alamitos, CA, USA, pp. 320-325.
28. Laub,M.T. et al. (2000) Global analysis of the genetic network controlling a bacterial cell cycle. Science, 290, 2144-2148.
29. Lelandais,G. et al. (2004) yMGV: A cross-species expression data mining tool. Nucleic Acids Res., 32, D323-D325.
30. Lelandais,G. et al. (2008) Genome adaptation to chemical stress: clues from comparative transcriptomics in Saccharomyces cerevisiae and Candida glabrata. Genome Biol., 9, R164.
31. Liao,B.Y. and Zhang,J. (2006a). Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution. Mol. Biol. Evol., 6, 1119-1128.
32. Liao,B.Y. and Zhang,J. (2006b) Evolutionary conservation of expression profiles between human and mouse orthologous genes. Mol. Biol. Evol. 23, 530-540.
33. Liu,Q. et al. (2007a) Comparative evaluation of gene-set analysis methods. BMC Bioinformatics, 8, 431.
34. Liu,M. et al. (2007b) Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet., 3 e96.
35. Lu,Y. et al. (2006). Identifying cycling genes by combining sequence homology and expression data. Bioinformatics, 22, e314-e322.
36. Lu,Y. et al. (2007a) Combined analysis reveals a core set of cycling genes. Genome Biol., 8, R146.
37. Lu,Y. et al. (2007b) Cross-species microarray analysis with the OSCAR system suggests an INSR-Pax6-NQO1 neuro-protective pathway in aging and Alzheimer's disease. Nucleic Acids Res., 35, W105-W114.
38. Manoli,T. et al. (2006) Group testing for pathway analysis improves comparability of different microarray datasets. Bioinformatics, 22, 2500-2506.
39. Menges,M. et al. (2002) Cell cycle-regulated gene expression in Arabidopsis. J. Biol. Chem., 277, 41987-42002.
40. Nau,G.J. et al. (2002) Human macrophage activation programs induced by bacterial pathogens. Proc. Natl Acad. Sci. USA, 99 1503-1508.
41. Newman,J. and Weiner,A. (2005) L2L: A simple tool for discovering the hidden significance in microarray expression data. Genome Biol., 6, R81.
42. Nuzhdin,S.V et al. (2004) Common pattern of evolution of gene expression level and protein sequence in drosophila. Mol. Biol. Evol. 21, 1308-1317.
43. Odom,O.T. et al. (2007) Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat. Genet., 39, 730-732.
44. Oliva,A. et al. (2005) The cell cycle-regulated genes of Schizosaccharomyces pombe. PLoS Biol., 3, e225.
45. Oshlack,A. et al. (2007) Using DNA microarrays to study gene expression in closely related species. Bioinformatics, 23, 1235.
46. Ota,K. et al. (2004) Comparative analysis of transcriptional regulation in eukaryotic cell cycles. In Proc. Fourth Int. Workshop Bioinf. Systems Biol., pp. 26-27.
47. Ramaswamy,S. et al. (2001) Multiclass cancer diagnosis using tumor gene expression signatures. Proc. Natl Acad. Sci. USA, 98, 15149-15154.
48. Rifkin,S.A. et al. (2003) Evolution of gene expression in the Drosophila melanogaster subgroup. Nat. Genet., 33, 138-144.
49. Rustici,G. et al. (2004) Periodic gene expression program of the fission yeast cell cycle. Nat. Genet., 36, 809-817.
50. Salomonis,N. et al. (2007) GenMAPP 2: New features and resources for pathway analysis. BMC Bioinformatics, 8, 217.
51. Sartor,M.A. et al. (2006) A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus. Nucleic Acids Res., 34 185.
52. Sharan,R. et al. (2005) Cover article: Conserved patterns of protein interaction in multiple species. Proc. Natl Acad. Sci. USA 8, 1974-1979.
53. Spellman,P.T. et al. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisia by microarray hybridization. Mol. Biol. Cell., 9, 3273-3297.
54. Stark,A. et al. (2003) Identification of drosophila microRNA targets. PLoS Biol., 1, e6.
55. Stuart,J.M. et al. (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science, 302, 249-255.
56. Su,A.I. et al. (2004). A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl Acad. Sci. USA, 101 6062-6067.
57. Subramanian,A. et al. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA, 102, 15545-15550.
58. Tirosh,I. et al. (2006) A genetic signature of interspecies variations in gene expression. Nat. Genet., 38, 830-834.
59. Ueda,H.R. et al. (2004). Universality and flexibility in gene expression from bacteria to human. Proc. Natl Acad. Sci. USA, 101, 3765-3769.
60. Vallee,M. et al. (2006) Cross-species hybridizations on a multi-species cDNA microarray to identify evolutionarily conserved genes expressed in oocytes. BMC Genomics, 7, 113.
61. Whitfeford,C.C. et al. (2007) Credentialing preclinical pediatric xenograft models using gene expression and tissue microarray analysis. Cancer Res., 67, 32-40.
62. Whitfield,M.L. et al. (2002) Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol. Biol. Cell, 13, 1977-2000.
63. Wilkins,A.S. (2001) The Evolution of Developmental Pathways. Sinauer Associates, Sunderland, MA, USA.
64. Xing,Y. et al. (2007). Assessing the conservation of mammalian gene expression using high-density exon arrays. Mol. Biol. Evol., 6, 1283-1285.
65. Yi,M. et al. (2006) Whole Pathway Scope: A comprehensive pathway-based analysis tool for high-throughput data. BMC Bioinformatics, 7, 30.