Inter-species differences of co-expression of neighboring genes in eukaryotic genomes

BMC Genomics

Volumn 5, Issue , 2004, Pages

  Fukuoka, Yutaka ^a   Inaoka, Hidenori ^a   Kohane, Isaac S ^b,c,d  

^a TOKYO MEDICAL AND DENTAL UNIVERSITY   (Japan)

^b BOSTON CHILDREN S HOSPITAL   (United States)

^c HARVARD UNIVERSITY   (United States)

^d Harvard Partners Center for Genetics and Genomics   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; ARTICLE; CAENORHABDITIS ELEGANS; CONTROLLED STUDY; DATA ANALYSIS; DROSOPHILA MELANOGASTER; EUKARYOTE; FUNGAL GENETICS; GENE CLUSTER; GENE DUPLICATION; GENE EXPRESSION; GENE ORDER; GENETIC ANALYSIS; GENETIC DISTANCE; GENETIC VARIABILITY; HUMAN; HUMAN CELL; MOUSE; NONHUMAN; RAT; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; SPECIES COMPARISON; SPECIES DIFFERENCE; WORM;

ANIMALS; CAENORHABDITIS ELEGANS; CHROMOSOME MAPPING; DROSOPHILA MELANOGASTER; EUKARYOTIC CELLS; GENE EXPRESSION; GENE ORDER; GENOME; HUMANS; MICE; PROTEINS; RATS; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; SPECIES SPECIFICITY;

DROSOPHILA MELANOGASTER; EUKARYOTA;

EID: 1842486262     PISSN: 14712164     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2164-5-4     Document Type: Article

References (32)

1. Cohen BA, Mitra RD, Hughes JD, Church GM: A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat Genet 2000, 26:183-186.
2. Kruglyak S, Tang H: Regulation of adjacent yeast genes. Trends in Genetics 2000, 16:109-111.
3. Lercher MJ, Blumenthal T, Hurst LD: Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes. Genome Res 2003, 13:238-243.
4. Lercher MJ, Urrutia AO, Hurst LD: Clustering of housekeeping genes provides a unified model of gene order in human genome. Nat Genet 2002, 31:180-183.
5. Roy PJ, Stuart JM, Lund J, Kim SK: Chromosomal clustering of muscle-expressed genes in Canenorhabditis elegans. Nature 2002, 418:975-979.
6. Spellman PT, Rubin GM: Evidence for large domains of similarly expressed genes in Drosophila genome. J Biol 2002, 1:5.
7. Boutanaev AM, Kalmykova AI, Shevelyov YY, Nurminsky DI: Large clusters of co-expressed genes in the Drosophila genome. Nature 2002, 420:666-669.
8. Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci 1998, 95:14863-14868.
9. Cho RJ, Fromont-Racine M, Wodicka L, Feierbach B, Stearns T, Legrain P, Lockhart DJ, Davis RW: Parallel analysis of genetic selections using whole genome oligonucleotide arrays. Proc Natl Acad Sci 1998, 95:3752-3757.
10. Montalta-He H, Leemans R, Loop T, Strahm M, Certa U, Primig M, Acampora D, Simeone A, Reichert H: Evolutionary conservation of otd/Otx2 transcription factor action: a genome-wide microarray analysis in Drosophila. Genome Biol 2002, 3:RESEARCH0015.
11. Egger B, Leemans R, Loop T, Kammermeier L, Fan Y, Radimerski T, Strahm MC, Certa U, Reichert H: Gliogenesis in Drosophila : genome-wide analysis of downstream genes of glial cells missing in the embryonic nervous system. Development 2002, 129:3295-3309.
12. Arbeitman MN, Furlong EE, Imam F, Johnson E, Null BH, Baker BS, Krasnow MA, Scott MP, Davis RW, White KP: Gene expression during life cycle of Drosophila melanogaster. Science 2002, 297:2270-2275.
13. Kim SK, Lund J, Kiraly M, Duke K, Jiang M, Stuart JM, Eizinger A, Wylie BN, Davidson GS: A gene expression map for Caenorhabditis elegans. Science 2001, 293:2087-2092.
14. Faden A: CNS Regeneration. [http://microarray.cnmcresearch.org/pgadatatable.asp].
15. Almon R: PGA Rat Liver Methylprednisolone. [http://microarray.cnmcresearch.org/pgadatatable.asp].
16. Almon R: PGA Rat Muscle Methylprednisolone. [http://microarray.cnmcresearch.org/pgadatatable.asp].
17. 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 2002, 99:4465-4470.
18. Schinke M, Riggi LE, Chen I, Izumo S: Exercise induced hypertrophy. [http://cardiogenomics.med.harvard.edu/groups/proj1/pages/swim_home.html]
19. Neptune ER: PGA Murine Fibrillin-1 Deficient. [http://microarray.cnmcresearch.org/pgadatatable.asp].
20. Scott A: PGA Alternatively Activated Macrophages, Massaro: PGA Murine Calories Restriction, O'Donnell C: PGA Murine Glucose Metabolism, Rose M: PGA Murine Goblet Cells, Kleeberger: PGA Murine Air Hyperpermability, Clerch: PGA Murine Lung Septation, Moller and Chen: PGA Murine Pulumonary Fibrosis, all at. [http://microarray.cnmcresearch.org/pgadatatable.asp].
21. Armstrong SA, Staunton JE, Silverman LB, Pieters R, den Boer ML, Minden MD, Sallan SE, Lander ES, Golub TR, Korsmeyer SJ: MLL translocations specify a distinct gene expression profile that distinguishers a unique leukemia. Nat Genet 2002, 30:41-47.
22. Pomeroy SL, Tamayo P, Gaasenbeek M, Sturla LM, Angelo M, McLaughlin ME, Kim JY, Goumnerova LC, Black PM, Lau C, Allen JC, Zagzag D, Olson JM, Curran T, Wetmore C, Biegel JA, Poggio T, Mukherjee S, Rifkin R, Califano A, Stolovitzky G, Louis DN, Mesirov JP, Lander ES, Golub TR: Prediction of central nervous system embryonal tumor outcome based on gene expression. Nature 2002, 415:436-442.
23. Ramaswamy S, Tamayo P, Rifkin R, Mukherjee S, Yeang CH, Angelo M, Ladd C, Reich M, Latulippe E, Mesirov JP, Poggio T, Gerald W, Loda M, Lander ES, Golub TR: Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci 2001, 98:15149-15154.
24. Yeoh EJ, Ross ME, Shurtleff SA, Williams WK, Patel D, Mahfouz R, Behm FG, Raimondi SC, Relling MV, Patel A, Cheng C, Campana D, Wilkins D, Zhou X, Li J, Liu H, Pui CH, Evans WE, Naeve C, Wong L, Downing JR: Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell 2002, 1:133-143.
25. Houmard JA: PGA Human Muscle Obese. [http://microarray.cnmcresearch.org/pgadatatable.asp].
26. Diette G: PGA Human CD4+Lymphocytes. [http://microarray.cnmcresearch.org/pgadatatable.asp].
27. Dyrskjot L, Thykjaer T, Kruhoffer M, Jensen JL, Marcussen N, Hamilton-Dutoit S, Wolf H, Orntoft TF: Identifying distinct classes of bladder carcinoma using microarrays. Nat Genet 2003, 33:90-96.
28. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J Jr, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, Staudt LM: Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000, 403:503-511.
29. Ryan TA: Significance tests for multiple comparison of proportions, variances, and other statistics. Psychological Bull 1960, 57:318-328.
30. Blumenthal T, Evans D, Link CD, Guffanti A, Lawson D, Thierry-Mieg J, Thierry-Mieg D, Chiu WL, Duke K, Kiraly M, Kim SK: A global analysis of Caenorhabditis elegans operons. Nature 2002, 417:851-854.
31. Alvarez M, Rhodes SJ, Bidwell JP: Context-dependent transcription: all politics is local. Gene 2003, 313:43-57.
32. Bell AC, West AG, Felsenfeld G: Insulators and boundaries: versatile regulatory elements in the eukaryotic genome. Science 2001, 291:447-450.