Differentially profiling the low-expression transcriptomes of human hepatoma using a novel SSH/microarray approach

BMC Genomics

Volumn 7, Issue , 2006, Pages

  Pan, Yi Shin ^a   Lee, Yun Shien ^a,c   Lee, Yung Lin ^a   Lee, Wei Chen ^a   Hsieh, Sen Yung ^a,b  

^a CHANG GUNG MEMORIAL HOSPITAL   (Taiwan)

^b CHANG GUNG UNIVERSITY   (Taiwan)

^c MING CHUAN UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA; TRANSCRIPTOME;

AMPLICON; ARTICLE; CELL CYCLE REGULATION; CELL DEATH; CONTROLLED STUDY; DNA HYBRIDIZATION; DNA MICROARRAY; FUNCTIONAL GENOMICS; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE SEQUENCE; GENE TARGETING; GENETIC TRANSCRIPTION; HUMAN; HUMAN TISSUE; LIVER CARCINOGENESIS; LIVER CELL CARCINOMA; MOLECULAR BIOLOGY; MORPHOGENESIS; QUANTITATIVE ASSAY; RANDOMIZATION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; STATISTICAL SIGNIFICANCE; SUPPRESSION SUBTRACTIVE HYBRIDIZATION; VALIDATION STUDY;

CARCINOMA, HEPATOCELLULAR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, NEOPLASM; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TRANSCRIPTION, GENETIC;

EID: 33746407595     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-131     Document Type: Article

References (31)

1. Schena M, Shalon D, Davis RW, Brown PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270:467-70.
2. Lockhart DJ, Dong H, Byrne C, 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. Nat Biotechnol 1996, 14:1675-80.
3. Wen X, Fuhrman S, Michaels GS, Carr DB, Smith S, Barker JL, Somogyi R: Large-scale temporal gene expression mapping of central nervous system development. Proc Natl Acad Sci USA 1998, 95:334-339.
4. Shyamsundar R, Kim YH, Higgins JP, Montgomery K, Jorden M, Sethuraman A, van de Rijn M, Botstein D, Brown PO, Pollack JR: A DNA microarray survey of gene expression in normal human tissues. Genome Biol 2005, 6:R22.
5. Diatchenko L, Lau YF, Campbell AP, Chenchik A, Moqadam F, Huang B, Lukyanov S, Lukyanov K, Gurskaya N, Sverdlov ED, Siebert PD: Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci USA 1996, 93:6025-30.
6. Diatchenko L, Lukyanov S, Lau Y, Siebert P: Suppression subtractive hybridization: a versatile method for identifying differentially expressed genes. Methods Enzymol 1999, 303:349-380.
7. Kuang WW, Thompson DA, Hoch RV, Weigel RJ: Differential screening and suppression subtractive hybridization identified genes differentiallyexpressed in an estrogen receptorpositive breast carcinoma cell line. Nucleic Acids Res 1998, 26:1116-23.
8. Harms C, Kase M, Hildebrandt A: Characterization of minute differences between genomes of strains of Penicillium nalgiovense using subtractive suppression hybridization without cloning. Lett Appl Microbiol 2002, 35:113-6.
9. Rebrikov DV, Desai SM, Siebert PD, Lukyanov SA: Suppression subtractive hybridization. Methods Mol Biol 2004, 258:107-34.
10. Yang GP, Ross DT, Kuang WW, Brown PO, Weigel RJ: Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes. Nucleic Acids Res 1999, 27:1517-23.
11. Welford SM, Gregg J, Chen E, Garrison D, Sorensen PH, Denny CT, Nelson SF: Detection of differentially expressed genes in primary tumor tissues using representational differences analysis coupled to microarray hybridization. Nucleic Acids Res 1998, 26:3059-65.
12. Amatschek S, Koenig U, Auer H, Steinlein P, Pacher M, Gruenfelder A, Dekan G, Vogl S, Kubista E, Heider KH, Stratowa C, Schreiber M, Sommergruber W: Tissue-wide expression profiling using cDNA subtraction and microarrays to identify tumor-specific genes. Cancer Res 2004, 64:844-56.
13. Bae JW, Rhee SK, Nam YD, Park YH: Generation of subspecies level-specific microbial diagnostic microarrays using genes amplified from subtractive suppression hybridization as microarray probes. Nucleic Acids Res 2005, 33:e113.
14. Rondeau G, McClelland M, Nguyen T, Risques R, Wang Y, Judex M, Cho AH, Welsh J: Enhanced microarray performance using low complexity representations of the transcriptome. Nucleic Acids Res 2005, 33:e100.
15. Rho J, Altmann CR., Socci ND, Merkov L, Kim N, So H, Lee O, Takami M, Brivanlou AH, Choi Y: Gene expression profiling of osteoclast differentiation by combined suppression subtractive hybridization (SSH) and cDNA microarray analysis. DNA Cell Biol 2002, 21:541-9.
16. Malyala A, Pattee P, Nagalla SR, Kelly MJ, Ronnekleiv OK: Suppression subtractive hybridization and microarrayidentification of estrogen-regulated hypothalamic genes. Neurochem Res 2004, 29:1189-200.
17. Munir S, Singh S, Kaur K, Kapur V: Suppression subtractive hybridization coupled with microarray analysis to examine differential expression of genes in virus infected cells. Biol Proced Online 2004, 6:94-104.
18. Hsieh SY, Chen WY, Shih TC, Yeh JY, Jeng JT: Dys-regulation of clusterin in human hepatoma is not associated with tumorigenesis but is secondary to cell response to external tresses. Mol Carcinog 2005, 43:100-7.
19. Feng HC., Tsao SW, Ngan HY, Kwan HS, Shih SM, Xue WC, Chiu PM, Chan KW, Cheung AN: Differential Gene Expression Identified in Complete Hydatidiform Mole by Combining Suppression Subtractive Hybridization and cDNA Microarray. Placenta 2005 in press.
20. Klebig C, Seitz S, Korsching E, Kristiansen G., Gustavus D, Scherneck S: Profile of differentially expressedgenes after transfer of chromosome 17 into the breast cancer cell line CAL51. Genes Chromosomes Cancer 2005, 44:233-46.
21. Seo EY, Namkung JH, Lee KM, Lee WH, Im M, Kee SH, Tae Park G, Yang JM, Seo YJ, Park JK, Deok Kim C, Lee JH: Analysis of calciuminducible genes in keratinocytes using suppression subtractive hybridizationand cDNA microarray. Genomics 2005, 86:528-38.
22. Vallee M, Gravel C, Palin MF, Reghenas H, Stothard P, Wishart DS, Sirard MA: Identification of novel and known oocyte-specific-genes using complementary DNA subtraction and microarray analysis inthree different species. Biol Reprod 2005, 73:63-71.
23. Ghorbel MT, Sharman G, Hindmarch C, Becker KG, Barrett T, Murphy D: Microarray screening of suppression subtractive hybridization-PCR cDNA libraries identifies novel RNAs regulated by dehydration in the rat supraoptic nucleus. Physiol Genomics 2006, 24:163-72.
24. Braun BS, Frieden R, Lessnick SL, May WA, Denny CT: Identification of target genes for the Ewing's sarcoma EWS/FLI fusion protein by representational difference analysis. Mol Cell Biol 1995, 15:4623-30.
25. Seta KA, Millhorn DE: Functional genomics approach to hypoxia signaling. J Appl Physiol 2004, 96:765-73.
26. Hsieh SY, Yang PY, Ou JT, Chu CM, Liaw YF: Polyadenylation of the mRNA of hepatitis delta virus is dependent on the structure of the nascent RNA and regulated by the small or large delta antigen. Nucleic Acids Res 1994, 22:391-6.
27. Hsieh SY, Liaw SF, Lee SN, Hsieh PS, Lin KH, Chu CM, Liaw YF: Aberrant Caspase-activated DNase (CAD) gene in human hepatoma cells. Br J Cancer 2003, 88:210-216.
28. Lee YS, Chen CH, Chao A, Chen ES, Wei ML, Chen LK, Yang KD, Lin MC, Wang YH, Liu JW, Eng HL, Chiang PC, Wu TS, Tsao KC, Huang CG, Tien YJ, Wang TH, Wang HS, Lee YS: Molecular signature of clinical severity in recovering patients with severe acute respiratory syndrome coronavirus (SARS-CoV). BMC Genomics 2005, 6:132.
29. FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes [http://fatigo.bio info.cipf.es/]
30. Bono H, Ogata H, Goto S, Kanehisa M: Reconstruction of amino acid biosynthesis pathways from the complete genome sequence. Genome Res 1998, 8:203-10.
31. KEGG 2: Kyoto Encyclopedia of Genes and Genomes [http://www.genome.ad.jp/kegg/]