Egger G, Liang G, Aparicio A, Jones PA: Epigenetics in human disease and prospects for epigenetic therapy. Nature. 2004, 429: 457-463. 10.1038/nature02625.
Article
CAS
PubMed
Google Scholar
Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, et al: Role of transposable elements in heterochromatin and epigenetic control. Nature. 2004, 430: 471-476. 10.1038/nature02651.
Article
CAS
PubMed
Google Scholar
Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M, Schubeler D: Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet. 2007, 39: 457-466. 10.1038/ng1990.
Article
CAS
PubMed
Google Scholar
Han L, Su B, Li W-H, Zhao Z: CpG island density and its correlations with genomic features in mammalian genomes. Genome Biol. 2008, 9: R79-10.1186/gb-2008-9-5-r79.
Article
PubMed Central
PubMed
Google Scholar
Han L, Zhao Z: Contrast features of CpG islands in the promoter and other regions in the dog genome. Genomics. 2009, 94: 117-124. 10.1016/j.ygeno.2009.04.007.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhao Z, Han L: CpG islands: algorithms and applications in methylation studies. Biochem Biophys Res Commun. 2009, 382: 643-645. 10.1016/j.bbrc.2009.03.076.
Article
PubMed Central
CAS
PubMed
Google Scholar
Robertson KD: DNA methylation and human disease. Nat Rev Genet. 2005, 6: 597-610.
Article
CAS
PubMed
Google Scholar
Szyf M: The role of DNA hypermethylation and demethylation in cancer and cancer therapy. Curr Oncol. 2008, 15: 72-75.
Article
PubMed Central
CAS
PubMed
Google Scholar
Szyf M, Pakneshan P, Rabbani SA: DNA methylation and breast cancer. Biochem Pharmacol. 2004, 68: 1187-1197. 10.1016/j.bcp.2004.04.030.
Article
CAS
PubMed
Google Scholar
Jaenisch R, Bird A: Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet. 2003, 33: 245-254. 10.1038/ng1089.
Article
CAS
PubMed
Google Scholar
Murrell A, Rakyan VK, Beck S: From genome to epigenome. Hum Mol Genet. 2005, 14: R3-R10. 10.1093/hmg/ddi110.
Article
CAS
PubMed
Google Scholar
Perez-Iratxeta C, Palidwor G, Porter CJ, Sanche NA, Huska MR, Suomela BP, Muro EM, Krzyzanowski PM, Hughes E, Campbell PA: Study of stem cell function using microarray experiments. FEBS Lett. 2005, 579: 1795-1801. 10.1016/j.febslet.2005.02.020.
Article
CAS
PubMed
Google Scholar
Wu X, Schmidt JA, Avarbock MR, Tobias JW, Carlson CA, Kolon TF, Ginsberg JP, Brinster RL: Prepubertal human spermatogonia and mouse gonocytes share conserved gene expression of germline stem cell regulatory molecules. Proc Natl Acad Sci USA. 2009, 106: 21672-21677. 10.1073/pnas.0912432106.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li Y, Zhu J, Tian G, Li N, Li Q, Ye M, Zheng H, Yu J, Wu H, Sun J, et al: The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol. 2010, 8 (11): e1000533-10.1371/journal.pbio.1000533.
Article
PubMed Central
PubMed
Google Scholar
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, et al: Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009, 462: 315-322. 10.1038/nature08514.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O'Malley R, Castanon R, Klugman S, et al: Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. 2011, 471 (7336): 68-73. 10.1038/nature09798.
Article
PubMed Central
CAS
PubMed
Google Scholar
Su Z, Han L, Zhao Z: Conservation and divergence of DNA methylation in eukaryotes: New insights from single base-resolution DNA methylomes. Epigenetics. 2011, 6: 134-140. 10.4161/epi.6.2.13875.
Article
PubMed Central
CAS
PubMed
Google Scholar
Filipowicz W, Bhattacharyya SN, Sonenberg N: Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?. Nat Rev Genet. 2008, 9: 102-114.
Article
CAS
PubMed
Google Scholar
Kozomara A, Griffiths-Jones S: miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 2011, 39: D152-D157. 10.1093/nar/gkq1027.
Article
PubMed Central
CAS
PubMed
Google Scholar
Griffiths-Jones S, Saini HK, Van Dongen S, Enright AJ: miRBase: tools for microRNA genomics. Nucleic Acids Res. 2008, 36: D154-D158. 10.1093/nar/gkn221.
Article
PubMed Central
CAS
PubMed
Google Scholar
Friedman LM, Dror AA, Mor E, Tenne T, Toren G, Satoh T, Biesemeier DJ, Shomron N, Fekete DM, Hornstein E, Avraham KB: MicroRNAs are essential for development and function of inner ear hair cells in vertebrates. Proc Natl Acad Sci USA. 2009, 106: 7915-7920. 10.1073/pnas.0812446106.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bushati N, Cohen SM: microRNA functions. Annu Rev Cell Dev Biol. 2007, 23: 175-205. 10.1146/annurev.cellbio.23.090506.123406.
Article
CAS
PubMed
Google Scholar
Jiang C, Han L, Su B, Li WH, Zhao Z: Features and trend of loss of promoter-associated CpG islands in the human and mouse genomes. Mol Biol Evol. 2007, 24: 1991-2000. 10.1093/molbev/msm128.
Article
CAS
PubMed
Google Scholar
Elango N, Hunt BG, Goodisman MA, Yi SV: DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis mellifera. Proc Natl Acad Sci USA. 2009, 106: 11206-11211. 10.1073/pnas.0900301106.
Article
PubMed Central
CAS
PubMed
Google Scholar
R package RmiR.hsa. [http://www.bioconductor.org/packages/2.8/data/annotation/html/RmiR.hsa.html]
McVicker G, Green P: Genomic signatures of germline gene expression. Genome Res. 2010, 20: 1503-10.1101/gr.106666.110.
Article
PubMed Central
CAS
PubMed
Google Scholar
Barberi T, Willis LM, Socci ND, Studer L: Derivation of multipotent mesenchymal precursors from human embryonic stem cells. PLoS Med. 2005, 2: e161-10.1371/journal.pmed.0020161.
Article
PubMed Central
PubMed
Google Scholar
Chalmel F, Rolland AD, Niederhauser-Wiederkehr C, Chung SSW, Demougin P, Gattiker A, Moore J, Patard JJ, Wolgemuth DJ, Jégou B: The conserved transcriptome in human and rodent male gametogenesis. Proc Natl Acad Sci USA. 2007, 104: 8346-8351. 10.1073/pnas.0701883104.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ge X, Yamamoto S, Tsutsumi S, Midorikawa Y, Ihara S, Wang SM, Aburatani H: Interpreting expression profiles of cancers by genome-wide survey of breadth of expression in normal tissues. Genomics. 2005, 86: 127-141. 10.1016/j.ygeno.2005.04.008.
Article
CAS
PubMed
Google Scholar
Houmard B, Small C, Yang L, Naluai-Cecchini T, Cheng E, Hassold T, Griswold M: Global gene expression in the human fetal testis and ovary. Biol Reprod. 2009, 81: 438-443. 10.1095/biolreprod.108.075747.
Article
PubMed Central
CAS
PubMed
Google Scholar
Looijenga LHJ, Hersmus R, Gillis AJM, Pfundt R, Stoop HJ, van Gurp RJ, Veltman J, Beverloo HB, van Drunen E, Geurts van Kessel A: Genomic and expression profiling of human spermatocytic seminomas: primary spermatocyte as tumorigenic precursor and DMRT1 as candidate chromosome 9 gene. Cancer Res. 2006, 66: 290-302. 10.1158/0008-5472.CAN-05-2936.
Article
CAS
PubMed
Google Scholar
Kocabas AM, Crosby J, Ross PJ, Otu HH, Beyhan Z, Can H, Tam WL, Rosa GJM, Halgren RG, Lim B: The transcriptome of human oocytes. Proc Natl Acad Sci USA. 2006, 103: 14027-14032. 10.1073/pnas.0603227103.
Article
PubMed Central
CAS
PubMed
Google Scholar
Korkola JE, Houldsworth J, Chadalavada RSV, Olshen AB, Dobrzynski D, Reuter VE, Bosl GJ, Chaganti R: Down-regulation of stem cell genes, including those in a 200-kb gene cluster at 12p13. 31, is associated with in vivo differentiation of human male germ cell tumors. Cancer Res. 2006, 66: 820-827. 10.1158/0008-5472.CAN-05-2445.
Article
CAS
PubMed
Google Scholar
Sato N, Sanjuan IM, Heke M, Uchida M, Naef F, Brivanlou AH: Molecular signature of human embryonic stem cells and its comparison with the mouse. Dev Biol. 2003, 260: 404-413. 10.1016/S0012-1606(03)00256-2.
Article
CAS
PubMed
Google Scholar
Skottman H, Mikkola M, Lundin K, Olsson C, Strömberg AM, Tuuri T, Otonkoski T, Hovatta O, Lahesmaa R: Gene expression signatures of seven individual human embryonic stem cell lines. Stem Cells. 2005, 23: 1343-1356. 10.1634/stemcells.2004-0341.
Article
CAS
PubMed
Google Scholar
Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, et al: A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci USA. 2004, 101: 6062-6067. 10.1073/pnas.0400782101.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hubbell E, Liu WM, Mei R: Robust estimators for expression analysis. Bioinformatics. 2002, 18: 1585-1592. 10.1093/bioinformatics/18.12.1585.
Article
CAS
PubMed
Google Scholar
BioGPS. [http://biogps.org]
Yang J, Su AI, Li WH: Gene expression evolves faster in narrowly than in broadly expressed mammalian genes. Mol Biol Evol. 2005, 22: 2113-2118. 10.1093/molbev/msi206.
Article
CAS
PubMed
Google Scholar
The Cancer Gene Census database. [http://www.sanger.ac.uk/genetics/CGP/Census/]
Volinia S, Mascellani N, Marchesini J, Veronese A, Ormondroyd E, Alder H, Palatini J, Negrini M, Croce CM: Genome wide identification of recessive cancer genes by combinatorial mutation analysis. PLoS One. 2008, 3: e3380-10.1371/journal.pone.0003380.
Article
PubMed Central
PubMed
Google Scholar
Xia J, Sun J, Jia P, Zhao Z: Do cancer proteins really interact strongly in the human protein-protein interaction network?. Comput Biol Chem. 2011, 35: 121-125. 10.1016/j.compbiolchem.2011.04.005.
Article
PubMed Central
PubMed
Google Scholar
Chen FC, Chen CJ, Li WH, Chuang TJ: Human-specific insertions and deletions inferred from mammalian genome sequences. Genome Res. 2007, 17: 16-22.
Article
PubMed Central
CAS
PubMed
Google Scholar
17-Way vertebrate alignment in the UCSC Genome Browser. [http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz17way/]
Deaton AM, Bird A: CpG islands and the regulation of transcription. Genes Dev. 2011, 25: 1010-1022. 10.1101/gad.2037511.
Article
PubMed Central
CAS
PubMed
Google Scholar
Illingworth RS, Gruenewald-Schneider U, Webb S, Kerr ARW, James KD, Turner DJ, Smith C, Harrison DJ, Andrews R, Bird AP: Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet. 2010, 6: e1001134-10.1371/journal.pgen.1001134.
Article
PubMed Central
PubMed
Google Scholar
Bird A: DNA methylation patterns and epigenetic memory. Genes Dev. 2002, 16: 6-21. 10.1101/gad.947102.
Article
CAS
PubMed
Google Scholar
Walsh CP, Bestor TH: Cytosine methylation and mammalian development. Genes Dev. 1999, 13: 26-34. 10.1101/gad.13.1.26.
Article
PubMed Central
CAS
PubMed
Google Scholar
Warnecke PM, Clark SJ: DNA methylation profile of the mouse skeletal alpha-actin promoter during development and differentiation. Mol Cell Biol. 1999, 19: 164-172.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wang X, El Naqa IM: Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics. 2008, 24: 325-332. 10.1093/bioinformatics/btm595.
Article
PubMed
Google Scholar
Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M: Combinatorial microRNA target predictions. Nat Genet. 2005, 37: 495-500. 10.1038/ng1536.
Article
CAS
PubMed
Google Scholar
Rajewsky N: microRNA target predictions in animals. Nat Genet. 2006, 38 (Suppl:): S8-S13.
Article
CAS
PubMed
Google Scholar
Cheng C, Bhardwaj N, Gerstein M: The relationship between the evolution of microRNA targets and the length of their UTRs. BMC Genomics. 2009, 10: 431-10.1186/1471-2164-10-431.
Article
PubMed Central
PubMed
Google Scholar
Kim SH, Yi SV: Understanding relationship between sequence and functional evolution in yeast proteins. Genetica. 2007, 131: 151-156. 10.1007/s10709-006-9125-2.
Article
CAS
PubMed
Google Scholar
Eisenberg E, Levanon EY: Human housekeeping genes are compact. Trends Genet. 2003, 19: 362-365. 10.1016/S0168-9525(03)00140-9.
Article
CAS
PubMed
Google Scholar
Stark A, Brennecke J, Bushati N, Russell RB, Cohen SM: Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution. Cell. 2005, 123: 1133-1146. 10.1016/j.cell.2005.11.023.
Article
CAS
PubMed
Google Scholar
Cui Q, Yu Z, Pan Y, Purisima EO, Wang E: MicroRNAs preferentially target the genes with high transcriptional regulation complexity. Biochem Biophys Res Commun. 2007, 352: 733-738. 10.1016/j.bbrc.2006.11.080.
Article
CAS
PubMed
Google Scholar
Xie X, Lu J, Kulbokas E, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M: Systematic discovery of regulatory motifs in human promoters and 3 UTRs by comparison of several mammals. Nature. 2005, 434: 338-345. 10.1038/nature03441.
Article
PubMed Central
CAS
PubMed
Google Scholar
PACdb. [http://harlequin.jax.org/pacdb/]
Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22: 4673-4680. 10.1093/nar/22.22.4673.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kimura M: A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980, 16: 111-120. 10.1007/BF01731581.
Article
CAS
PubMed
Google Scholar
Sun J, Zhao Z: A comparative study of cancer proteins in the human protein-protein interaction network. BMC Genomics. 2010, 11 (Suppl): S3-S5. 10.1186/1471-2164-11-S3-S5.
Google Scholar
Gu X, Su Z, Huang Y: Simultaneous expansions of microRNAs and protein-coding genes by gene/genome duplications in early vertebrates. J Exp Zool B Mol Dev Evol. 2009, 312B: 164-170. 10.1002/jez.b.21273.
Article
CAS
PubMed
Google Scholar
Heimberg AM, Sempere LF, Moy VN, Donoghue PC, Peterson KJ: MicroRNAs and the advent of vertebrate morphological complexity. Proc Natl Acad Sci USA. 2008, 105: 2946-2950. 10.1073/pnas.0712259105.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mandrioli M: A new synthesis in epigenetics: towards a unified function of DNA methylation from invertebrates to vertebrates. Cell Mol Life Sci. 2007, 64: 2522-2524. 10.1007/s00018-007-7231-7.
Article
CAS
PubMed
Google Scholar