Exploiting orthologue diversity for systematic detection of gain-of-function phenotypes

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Martelli, Maria Luisa ^a   Isella, Claudio ^a   Mira, Alessia ^a   Fu, Limin ^a   Cantarella, Daniela ^a   Medico, Enzo ^a  

^a UNIVERSITY OF TURIN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; ARTICLE; CELL ANCHORAGE; CELL CULTURE; CELL GROWTH; CELL STRAIN; CONTROLLED STUDY; CROSS HYBRIDIZATION; DNA MICROARRAY; GENE FUNCTION; GENETIC GAIN; GENETIC SCREENING; GENETIC TRANSDUCTION; GENETIC VARIABILITY; HELA CELL; HUMAN; HUMAN CELL; MOLECULAR CLONING; MOUSE; NONHUMAN; ORTHOLOGY; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; ANIMAL; CELL LINE; DOG; FEASIBILITY STUDY; GENE LIBRARY; GENETICS; MALE; METABOLISM; PHENOTYPE; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; TESTIS;

MAMMALIA; MURINAE;

DNA BINDING PROTEIN; NUCLEAR PROTEIN; SOX5 PROTEIN, MOUSE;

ANIMALS; CELL LINE; DNA-BINDING PROTEINS; DOGS; FEASIBILITY STUDIES; GENE LIBRARY; HUMANS; MALE; MICE; NUCLEAR PROTEINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY; TESTIS; TRANSDUCTION, GENETIC; VARIATION (GENETICS);

EID: 46049095477     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-254     Document Type: Article

References (39)

1. Aruffo A Expression cloning systems Curr Opin Biotechnol 1991, 2:735-741 10.1016/0958-1669(91)90044-6 1367727
2. Kitamura T Koshinoa Y Shibata F Okia T Nakajima H Nosakab T Kumagai H Retrovirus-mediated gene transfer and expression cloning: Powerful tools in functional genomics Exp Hematol 2003, 31:1007-1014 14585362
3. Nakayama N Yokota T Arai K Use of mammalian cell expression cloning systems to identify genes for cytokines, receptors, and regulatory proteins Curr Opin Biotechnol 1992, 3:497-505 10.1016/ 0958-1669(92)90077-V 1369401
4. Simonsen H Lodish HF Cloning by function: Expression cloning in mammalian cells Trends Pharmacol 1994, 15:437-441 10.1016/ 0165-6147(94)90052-3
5. Peeper DS Shvarts A Brummelkamp T Douma S Koh EY Daley GQ Bernards R A functional screen identifies hDRIL1 as an oncogene that rescues RAS-induced senescence Nat Cell Biol 2002, 4:148-153 10.1038/ncb742 11812999
6. Hannon GJ Sun P Carnero A Xie LW Maestro R Conklin DS Beach D MaRX: An Approach to Genetics in Mammalian Cells Science 1999, 283:1129-1130 10.1126/science.283.5405.1129 10075573
7. Shoemaker DD Lashkari DA Morris D Mittmann M Davis RV Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy Nature Genetics 1996, 14:450-456 10.1038/ ng1296-450 8944025
8. Berns K Hijmans EM Mullenders J Brummelkamp TR Velds A Heimerikx M Kerkhoven RM Madiredjo M Nijkamp W Weigelt B Agami R Ge W Cavet G Linsley PS Beijersbergen RL Bernards R A large-scale RNAi screen in human cells identifies new components of the p53 pathway Nature 2004, 428:431-437 10.1038/nature02371 15042092
9. Silva JM Li MZ Chang K Ge W Golding MC Rickles RJ Siolas D Hu G Paddison PJ Schlabach MR Sheth N Bradshaw J Burchard J Kulkarni A Cavet G Sachidanandam R McCombie WR Cleary MA Elledge SJ Hannon GJ Second-generation shRNA libraries covering the mouse and human genomes Nat Genet 2005, 11:1281-1288 10.1038/nm1205-1281
10. Mouse Genome Sequencing Consortium Waterston RH Lindblad-Toh K Birney E Rogers J Abril JF Agarwal P Agarwala R Ainscough R Alexandersson M An P Antonarakis SE Attwood J Baertsch R Bailey J Barlow K Beck S Berry E Birren B Bloom T Bork P Botcherby M Bray N Brent MR Brown DG Brown SD Bult C Burton J Butler J Campbell RD Carninci P Initial sequencing and comparative analysis of the mouse genome Nature 2002, 420:520-562 10.1038/nature01262 12466850
11. Velculescu VE Zhang L Vogelstein B Kinzler KW Serial analysis of gene expression Science 1995, 270:484-487 10.1126/science.270.5235.484 7570003
12. Siddiqui AS Khattra J Delaney AD Zhao Y Astell C Asano J Babakaiff R Barber S Beland J Bohacec S Brown-John M Chand S Charest D Charters AM Cullum R Dhalla N Featherstone R Gerhard DS Hoffman B Holt RA Hou J Kuo BY Lee LL Lee S Leung D Ma K Matsuo C Mayo M McDonald H Prabhu AL A mouse atlas of gene expression: Large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells Proc Natl Acad Sci USA 2005, 102:18485-18490 1311911 16352711 10.1073/pnas.0509455102
13. Paul D Growth control in HeLa cells by serum and anchorage Exp Cell Res 1978, 114:435-438 10.1016/0014-4827(78)90503-7 679993
14. Macville M Schrock E Padilla-Nash H Keck C Ghadimi BM Zimonjic D Popescu N Ried T Comprehensive and definitive molecular cytogenetic characterization of HeLa cells by spectral karyotyping Cancer Res 1999, 59(1):141-150 9892199
15. Frisch SM Francis H Disruption of epithelial cell-matrix interactions induces apoptosis J Cell Biol 1994, 124:619-626 2119917 8106557 10.1083/ jcb.124.4.619
16. Mantovani J Holic N Martinez K Danos O Perea J A high throughput method for genome-wide analysis of retroviral integration Nucleic Acids Res 2006, 34:e134 1636494 17028098 10.1093/nar/gkl716
17. Schubbert S Shannon K Bollag G Hyperactive Ras in developmental disorders and cancer Nat Rev Cancer 2007, 7:295-308 10.1038/nrc2109 17384584
18. Singh B Arlinghaus RB The mos proto-oncogene product: Its role in oocyte maturation, metaphase arrest, and neoplastic transformation Mol Carcinog 1992, 3:182-189 10.1002/mc.2940060303
19. Dufault VM Oestreich AJ Vroman BT Karnitz LM Identification and characterization of RAD9B, a paralog of the RAD9 checkpoint gene Genomics 2003, 6:644-651 10.1016/S0888-7543(03)00200-3
20. Hiraoka Y Ogawa M Sakai Y Kido S Aiso S The mouse Sox5 gene encodes a protein containing the leucine zipper and the Q box Biochim Biophys Acta 1998, 1399(1):40-46 9714725
21. Wunderle VM Critcher R Ashworth A Goodfellow PN Cloning and characterization of SOX5, a new member of the human SOX gene family Genomics 1996, 2:354-358 10.1006/geno.1996.0474
22. Smits P Li P Mandel J Zhang Z Deng JM Behringer RR de Crombrugghe B Lefebvre V The transcription factors L-Sox5 and Sox6 are essential for cartilage formation Dev Cell 2001, 2:277-290 10.1016/ S1534-5807(01)00003-X
23. Ueda R Yoshida K Kawakami Y Kawase T Toda M Expression of a transcriptional factor, SOX6, in human gliomas Brain Tumor Pathol 2004, 1:35-38 10.1007/BF02482175
24. Ueda R Yoshida K Kawase T Kawakami Y Toda M Preferential expression and frequent IgG responses of a tumor antigen, SOX5, in glioma patients Int J Cancer 2007, 8:1704-1711 10.1002/ijc.22472
25. Iguchi H Urashima Y Inagaki Y Ikeda Y Okamura M Tanaka T Uchida A Yamamoto TT Kodama T Sakai J SOX6 suppresses cyclin D1 promoter activity by interacting with beta-catenin and histone deacetylase 1, and its down-regulation induces pancreatic beta-cell proliferation J Biol Chem 2007, 26:19052-19061 10.1074/jbc.M700460200
26. Zafarana G Gillis AJ van Gurp RJ Olsson PG Elstrodt F Stoop H Millán JL Oosterhuis JW Looijenga LH Coamplification of DAD-R, SOX5, and EKI1 in human testicular seminomas, with specific overexpression of DAD-R, correlates with reduced levels of apoptosis and earlier clinical manifestation Cancer Res 2002, 62(6):1822-1831 11912161
27. Storlazzi CT Albano F Lo Consolo C Dogliosi C Guastadisegni MC Impera L Lonoce A Funes S Macrì E Iuzzolino P Panagopoulos I Specchia G Rocchi M Upregulation of the SOX5 by promoter swapping with the P2RY8 gene in primary splenic follicular lymphoma Leukemia 2007, 21(10):2221-2225 10.1038/sj.leu.2404784 17554380
28. Schena M Shalon D Davis RW Brown PO Quantitative monitoring of gene expression patterns with a complementary DNA microarray Science 1995, 270:467-470 10.1126/science.270.5235.467 7569999
29. Lockhart DJ Dong H Byrne MC Follettie MT Gallo MV Chee MS Mittmann M Wang C Kobayashi M Horton H Brown EL Expression monitoring by hybridization to high-density oligonucleotide arrays Nature Biotechnol 1996, 14:1675-1678 10.1038/nbt1296-1675
30. Berns K Horlings HM Hennessy BT Madiredjo M Hijmans EM Beelen K Linn SC Gonzalez-Angulo AM Stemke-Hale K Hauptmann M Beijersbergen RL Mills GB Vijver van de MJ Bernards R A Functional Genetic Approach Identifies the PI3K Pathway as a Major Determinant of Trastuzumab Resistance in Breast Cancer Cancer Cell 2007, 12:395-402 10.1016/j.ccr.2007.08.030 17936563
31. Heinicke S Livstone MS Lu C Oughtred R Kang F Angiuoli SV White O Botstein D Dolinski K The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists PLoS ONE 2007, 2:766 10.1371/journal.pone.0000766
32. Hurlin PJ Fry DG Maher VM McCormick JJ Morphological transformation, focus formation, and anchorage independence induced in diploid human fibroblasts by expression of a transfected H-ras oncogene Cancer Res 1987, 47:5752-5757 2444334
33. Bos JL The ras gene family and human carcinogenesis Mutat Res 1988, 195:255-271 3283542
34. Shetty S Regulation of urokinase receptor mRNA stability by hnRNP C in lung epithelial cells Mol Cell Biochem 2005, 272:107-118 10.1007/ s11010-005-7644-2 16010978
35. Pillay V Dass CR Choong PF The urokinase plasminogen activator receptor as a gene therapy target for cancer Trends Biotechnol 2007, 25:33-39 10.1016/j.tibtech.2006.10.011 17084931
36. Edwards AS Scott JD A-kinase anchoring proteins: Protein kinase A and beyond Curr Opin Cell Biol 2000, 12:217-221 10.1016/ S0955-0674(99)00085-X 10712918
37. Yoshida Y Tokunaga F Chiba T Iwai K Tanaka K Tai T Fbs2 is a new member of the E3 ubiquitin ligase family that recognizes sugar chains J Biol Chem 2003, 278:43877-43884 10.1074/jbc.M304157200 12939278
38. Trolltech website http://www.trolltech.com
39. Xas project page on Sourceforge http://www.sourceforge.net/projects/xas