Genomic technologies and the interrogation of the transcriptome

Mechanisms of Ageing and Development

Volumn 126, Issue 1, 2005, Pages 153-159

  Liu, Edison T ^a  

^a GENOME INSTITUTE OF SINGAPORE   (Singapore)

Author keywords

cDNA; Genome; Transcriptome

Indexed keywords

COMPLEMENTARY DNA;

AGING; CANCER GENETICS; CHROMATIN; CONFERENCE PAPER; DNA MICROARRAY; GENE EXPRESSION; GENE TECHNOLOGY; GENETIC REGULATION; GENETIC TRANSCRIPTION; GENOME; GENOMICS; HUMAN; IMMUNOPRECIPITATION; NONHUMAN; NORTHERN BLOTTING; PRIORITY JOURNAL; PROTEOMICS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

ANIMALS; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; TRANSCRIPTION, GENETIC;

EID: 10944259926     PISSN: 00476374     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mad.2004.09.027     Document Type: Conference Paper

References (46)

1. M. Adams, M.D. Adams, J.M. Kelley, J.D. Gocayne, M. Dubnick, and M.H. Polymeropoulos Complementary DNA sequencing: expressed sequence tags and human genome project Science 252 1991 1651 1656
2. T.J. Albert, J. Norton, M. Ott, T. Richmond, K. Nuwaysir, and E.F. Nuwaysir Light-directed 5′ → 3′ synthesis of complex oligonucleotide microarrays Nucleic Acids Res. 31 7 2003 e35
3. O. Aprelikova, A.J. Pace, B. Fang, B.H. Koller, and E.T. Liu BRCA1 is a selective co-activator of 14-3-3 sigma gene transcription in mouse embryonic stem cells J. Biol. Chem. 276 28 2001 25647 25650
4. M.M. Babu, N.M. Luscombe, L. Aravind, M. Gerstein, and S.A. Teichmann Structure and evolution of transcriptional regulatory networks Curr. Opin. Struct. Biol. 14 2004 283 291
5. S. Brenner, and K.J. Livak DNA fingerprinting by sampled sequencing Proc. Natl. Acad. Sci. USA 86 22 1989 8902 8906
6. S. Brenner, S.R. Williams, E.H. Vermaas, T. Storck, K. Moon, and C. McCollum In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs PNAS 97 2000 1665 1670
7. S. Brenner, M. Johnson, J. Bridgham, G. Golda, D.H. Lloyd, and D. Johnson Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays Nat. Biotechnol. 18 2000 630 634
8. P. Carninci, C. Kvam, A. Kitamura, T. Ohsumi, Y. Okazaki, and M. Itoh High-efficiency full-length cDNA cloning by biotinylated CAP trapper Genomics 37 1996 327 336
9. P. Carninci, Y. Shibata, N. Hayatsu, Y. Sugahara, K. Shibata, and M. Itoh Normalization and subtraction of cap-trapper selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes Genome Res. 10 2000 1617 1630
10. S. Cawley, S. Cawley, S. Bekiranov, H.H. Ng, P. Kapranov, and E.A. Sekinger Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs Cell 116 2004 499 509
11. E.H. Davidson, J.P. Rast, P. Oliveri, A. Ransick, C. Calestani, and C.H. Yuh A genomic regulatory network for development Science 295 5560 2002 1669 1678
12. E.H. Davidson, J.P. Rast, P. Oliveri, A. Ransick, C. Calestani, and C.H. Yuh A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo Dev. Biol. 246 1 2002 162 190
13. K.V. Desai, N. Xiao, W. Wang, L. Gangi, J. Greene, and J.I. Powell Initiating oncogenic event determines gene-expression patterns of human breast cancer models Proc. Natl. Acad. Sci. USA 99 2002 6967 6972
14. S.M. Dhanasekaran, T.R. Barrette, D. Ghosh, R. Shah, S. Varambally, and K. Kurachi Delineation of prognostic biomarkers in prostate cancer Nature 412 6849 2001 822 826
15. E. Dias Neto, R.G. Correa, S. Verjovski-Almeida, M.R. Briones, M.A. Nagai, and W. Da Silva Jr. Shotgun sequencing of the human transcriptome with ORF expressed sequence tags Proc. Natl. Acad. Sci. USA 97 2000 3491 3496
16. M.B. Eisen, and P.O. Brown DNA arrays for analysis of gene expression S.M. Weissman Methods in Enzymology: cDNA Preparation and Characterization vol. 303 1999 Academic Press 179 205
17. G. Euskirchen, T.E. Royce, P. Bertone, R. Martone, J.L. Rinn, and F.K. Nelson CREB binds to multiple loci on human chromosome 22 Mol. Cell. Biol. 24 9 2004 3804 3814
18. N. Guelzim, S. Bottani, P. Bourgine, and F. Kepes Topological and causal structure of the yeast transcriptional regulatory network Nature Genet. 31 1 2002 60 63
19. C.A. Harrington, Carsten Rosenow, and Jacques Retief Monitoring gene expression using DNA microarrays Curr. Opin. Microbiol. 3 2000 285 291
20. C.E. Horak, and M. Snyder Methods Enzymol. 350 2002 469 483
21. C.E. Horak, N.M. Luscombe, J. Qian, P. Bertone, S. Piccirrillo, and M. Gerstein Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae Genes Dev. 16 23 2002 3017 3033
22. J.M. Johnson, J. Castle, P. Garrett-Engele, Z. Kan, P.M. Loerch, and C.D. Armour Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays Science 302 5653 2003 2141 2144
23. D. Kampa, J. Cheng, P. Kapranov, M. Yamanaka, S. Brubaker, and S. Cawley Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22 Genome Res. 14 3 2004 331 342
24. P. Karpranov, S.E. Cawley, J. Drenkow, S. Bekiranov, R.L. Strausberg, and S.P. Fodor Large-scale transcriptional activity in chromosomes 21 and 22 Science 296 2002 916 919
25. H. Kiyosawa Antisense transcripts with FANTOM2 clone set and their implications for gene regulation Genome Res. 13 6B 2003 1324 1334
26. B. Lehner, G. Williams, R.D. Campbell, and C.M. Sanderson Antisense transcripts in the human genome Trends Genet. 18 2 2002 63 65
27. C.Y. Lin, A. Strom, V.B. Vega, S. Li Kong, A. Li Yeo, and J.S. Thomsen Discovery of estrogen receptor alpha target genes and response elements in breast tumor cells Genome Biol. 5 9 2004 66
28. R.J. Lipshutz, S.P.A. Fodor, T.R. Gingeras, and D.J. Lockhart High density synthetic oligonucleotide arrays Suppl. Nat. Genet. 21 1999 20 24
29. R. Martone, G. Euskirchen, P. Bertone, S. Hartman, T.E. Royce, and N.M. Luscombe Distribution of NF-kappaB-binding sites across human chromosome 22 Proc. Natl. Acad. Sci. USA 100 21 2003 12247 12252
30. L.D. Miller, K.S. Park, Q.M. Guo, N.W. Alkharouf, R.L. Malek, and N.H. Lee Silencing of Wnt signaling and activation of multiple metabolic pathways in response to thyroid hormone-stimulated cell proliferation Mol. Cell. Biol. 21 19 2001 6626 6639
31. L.D. Miller, P.M. Long, L. Wong, S. Mukherjee, L.M. McShane, and E.T. Liu Optimal gene expression analysis by microarrays Cancer Cell 2 5 2002 353 361
32. V.K. Mootha, C.M. Lindgren, K.F. Eriksson, A. Subramanian, S. Sihag, and J. Lehar PGC-1 alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes Nat. Genet. 34 3 2003 267 273
33. Y. Okazaki Analysis of the mouse transcriptome based on functional annotation of 60 770 full-length cDNAs Nature 420 2002 563 573
34. T. Ota, Y. Suzuki, T. Nishikawa, T. Otsuki, T. Sugiyama, and R. Irie Complete sequencing and characterization of 21 243 full-length human cDNAs Nat. Genet. 36 1 2004 40 45
35. J.L. Rinn, G. Euskirchen, P. Bertone, R. Martone, N.M. Luscombe, and S. Hartman The transcriptional activity of human Chromosome 22 Genes Dev. 17 4 2003 529 540
36. Y. Ruan, P. Le Ber, H.H. Ng, and E.T. Liu Interrogating the transcriptome Trends Biotechnol. 22 1 2004 23 30
37. S. Saha, A.B. Sparks, C. Rago, V. Akmaev, C.J. Wang, and B. Vogelstein Using the transcriptome to annotate the genome Nat. Biotechnol. 20 2002 508 512
38. F. Schweighoffer et al. 2004. Qualitative differential screening, Patent Application WO99/46403.
39. C. Sotiriou, S.Y. Neo, L.M. McShane, E.L. Korn, P.M. Long, and A. Jazaeri Breast cancer classification and prognosis based on gene expression profiles from a population-based study Proc. Natl. Acad. Sci. USA 100 18 2003 10393 10398
40. R.L. Stears, T. Martinsky, and M. Schena Trends in microarray analysis Nat. Med. 9 1 2003 140 145
41. V.E. Velculescu, L. Zhang, B. Vogelstein, and K.W. Kinzler Serial analysis of gene expression Science 270 1995 484 487
42. S. Varambally, S.M. Dhanasekaran, M. Zhou, T.R. Barrette, C. Kumar-Sinha, and M.G. Sanda The polycomb group protein EZH2 is involved in progression of prostate cancer Nature 419 6907 2002 624 629 Oct 10
43. E.G. Wagner, and R.W. Simons Antisense RNA control in bacteria, phages, and plasmids Annu. Rev. Microbiol. 48 1994 713 742
44. C.L. Wei, P. Ng, K.P. Chiu, C.H. Wong, C.C. Ang, and L. Lipovich 5′ Long serial analysis of gene expression (LongSAGE) and 3′ LongSAGE for transcriptome characterization and genome annotation Proc. Natl. Acad. Sci. USA 101 32 2004 11701 11706 Epub 22 July 2004.
45. K. Yamada Empirical analysis of transcriptional activity in the Arabidopsis genome Science 302 5646 2003 842 846
46. R. Yelin, D. Dahary, R. Sorek, E.Y. Levanon, O. Goldstein, and A. Shoshan Widespread occurrence of antisense transcription in the human genome Nat. Biotechnol. 21 4 2003 379 386