A gene family-based method for interspecies comparisons of sequencing-based transcriptomes and its use in environmental adaptation analysis

Journal of Genetics and Genomics - Tập 37 - Trang 205-218 - 2010
Zuozhou Chen1, Hua Ye1, Longhai Zhou1, Chi-Hing C. Cheng2, Liangbiao Chen1
1Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
2Department of Animal Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

Tài liệu tham khảo

Abele, 2004, Formation of reactive species and induction of antioxidant defence systems in polar and temperate marine invertebrates and fish, Comp. Biochem. Physiol. A Mol. Integr. Physiol., 138, 405, 10.1016/j.cbpb.2004.05.013 Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2 Ashburner, 2000, Gene ontology: tool for the unification of biology. The Gene Ontology Consortium, Nat. Genet., 25, 25, 10.1038/75556 Audic, 1997, The significance of digital gene expression profiles, Genome Res., 7, 986, 10.1101/gr.7.10.986 Benjamini, 1995, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. Roy. Stat. Soc. B, 57, 289 Binkert, 1999, Regulation of osteogenesis by fetuin, J. Biol. Chem., 274, 28514, 10.1074/jbc.274.40.28514 Boguski, 1993, dbEST—database for “expressed sequence tags”, Nat. Genet., 4, 332, 10.1038/ng0893-332 Brenner, 2000, Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays, Nat. Biotechnol., 18, 630, 10.1038/76469 Caceres, 2003, Elevated gene expression levels distinguish human from non-human primate brains, Proc. Natl. Acad. Sci. USA, 100, 13030, 10.1073/pnas.2135499100 Chen, 2007, Evolutionary-conserved gene expression response profiles across mammalian tissues, Omics, 11, 96, 10.1089/omi.2006.0007 Chen, 2006, GO-Diff: mining functional differentiation between EST-based transcriptomes, BMC Bioinformatics, 7, 72, 10.1186/1471-2105-7-72 Chen, 2005, GoPipe: streamlined gene ontology annotation for batch anonymous sequences with statistics, Prog. Biochem. Biophy., 32, 187 Chen, 2008, Transcriptomic and genomic evolution under constant cold in Antarctic notothenioid fish, Proc. Natl. Acad. Sci. USA, 105, 12944, 10.1073/pnas.0802432105 Clarke, 1984, Lipid content and composition of three species of Antarctic fish in relation to buoyancy, Polar Biol., 3, 77, 10.1007/BF00258151 Eastman, 1981, Buoyancy adaptations in a swim-bladderless Antarctic fish, J. Morph., 167, 91, 10.1002/jmor.1051670108 Eastman, 1982, Buoyancy studies of notothenioid fishes in McMurdo Sound, Antarctica, Copeia, 2, 385, 10.2307/1444619 Enard, 2002, Intra- and interspecific variation in primate gene expression patterns, Science, 296, 340, 10.1126/science.1068996 Ewing, 1998, Base-calling of automated sequencer traces using phred. II. Error probabilities, Genome Res., 8, 186, 10.1101/gr.8.3.175 Fei, 2004, Comprehensive EST analysis of tomato and comparative genomics of fruit ripening, Plant J., 40, 47, 10.1111/j.1365-313X.2004.02188.x Finn, 2008, The Pfam protein families database, Nucleic Acids Res., 36, D281, 10.1093/nar/gkm960 Gilad, 2005, Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles, Genome Res., 15, 674, 10.1101/gr.3335705 Gilad, 2006, Expression profiling in primates reveals a rapid evolution of human transcription factors, Nature, 440, 242, 10.1038/nature04559 Gu, 2007, Tissue-driven hypothesis of genomic evolution and sequence-expression correlations, Proc. Natl. Acad. Sci. USA, 104, 2779, 10.1073/pnas.0610797104 Heiss, 2003, Structural basis of calcification inhibition by alpha 2-HS glycoprotein/fetuin-A. Formation of colloidal calciprotein particles, J. Biol. Chem., 278, 13333, 10.1074/jbc.M210868200 Hoffmann, 2007, Neutrality, compensation, and negative selection during evolution of B-cell development transcriptomes, Mol. Biol. Evol., 24, 2610, 10.1093/molbev/msm198 Huang, 1999, CAP3: a DNA sequence assembly program, Genome Res., 9, 868, 10.1101/gr.9.9.868 Hunter, 2008, InterPro: the integrative protein signature database, Nucleic Acids Res., 21, 21 Khaitovich, 2005, Toward a neutral evolutionary model of gene expression, Genetics, 170, 929, 10.1534/genetics.104.037135 Khaitovich, 2006, Evolution of primate gene expression, Nat. Rev. Genet., 7, 693, 10.1038/nrg1940 Khaitovich, 2004, A neutral model of transcriptome evolution, PLoS Biol., 2, E132, 10.1371/journal.pbio.0020132 Khaitovich, 2005, Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees, Science, 309, 1850, 10.1126/science.1108296 Khatri, 2005, Ontological analysis of gene expression data: current tools, limitations, and open problems, Bioinformatics, 21, 3587, 10.1093/bioinformatics/bti565 Lemos, 2005, Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions, Mol. Biol. Evol., 22, 1345, 10.1093/molbev/msi122 Liang, 2000, An optimized protocol for analysis of EST sequences, Nucleic Acids Res., 28, 3657, 10.1093/nar/28.18.3657 Liao, 2006, Evolutionary conservation of expression profiles between human and mouse orthologous genes, Mol. Biol. Evol., 23, 530, 10.1093/molbev/msj054 Liao, 2006, Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution, Mol. Biol. Evol., 23, 1119, 10.1093/molbev/msj119 Man, 2000, POWER_SAGE: comparing statistical tests for SAGE experiments, Bioinformatics, 16, 953, 10.1093/bioinformatics/16.11.953 Margulies, 2005, Genome sequencing in microfabricated high-density picolitre reactors, Nature, 437, 376, 10.1038/nature03959 Marioni, 2008, RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays, Genome Res., 18, 1509, 10.1101/gr.079558.108 Metcalf, 1999, The Antarctic toothfish (Dissostichus mawsoni) lacks plasma albumin and utilises high density lipoprotein as its major palmitate binding protein, Comp. Biochem. Physiol. B Biochem. Mol. Biol., 124, 147, 10.1016/S0305-0491(99)00051-6 Meyers, 2004, Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing, Nat. Biotechnol., 22, 1006, 10.1038/nbt992 Nobuta, 2007, Methods for analysis of gene expression in plants using MPSS, Methods Mol. Biol., 406, 387, 10.1007/978-1-59745-535-0_19 Redon, 2006, Global variation in copy number in the human genome, Nature, 444, 444, 10.1038/nature05329 Sutton, 1995, TIGR Assembler: a new tool for assembling large shotgun sequencing projects, Genome Sci. Tech., 1, 9, 10.1089/gst.1995.1.9 Suzek, 2007, UniRef: comprehensive and non-redundant UniProt reference clusters, Bioinformatics, 23, 1282, 10.1093/bioinformatics/btm098 t Hoen, 2008, Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms, Nucleic Acids Res., 36, e141, 10.1093/nar/gkn705 Tirosh, 2008, Evolution of gene sequence and gene expression are not correlated in yeast, Trends Genet., 24, 109, 10.1016/j.tig.2007.12.004 van Ruissen, 2007, Serial analysis of gene expression (SAGE), Methods Mol. Biol., 383, 41, 10.1007/978-1-59745-335-6_4 Whitehead, 2006, Neutral and adaptive variation in gene expression, Proc. Natl. Acad. Sci. USA, 103, 5425, 10.1073/pnas.0507648103 Wu, 2006, The Universal Protein Resource (UniProt): an expanding universe of protein information, Nucleic Acids Res., 34, D187, 10.1093/nar/gkj161