메뉴 건너뛰기




Volumn 2, Issue 4, 2006, Pages 492-497

Genome Network and FANTOM3: Assessing the complexity of the transcriptome

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA; TRANSCRIPTOME;

EID: 33646486093     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0020063     Document Type: Editorial
Times cited : (28)

References (47)
  • 3
    • 21044431735 scopus 로고    scopus 로고
    • Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution
    • Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, et al. (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308: 1149-1154.
    • (2005) Science , vol.308 , pp. 1149-1154
    • Cheng, J.1    Kapranov, P.2    Drenkow, J.3    Dike, S.4    Brubaker, S.5
  • 4
    • 19944376457 scopus 로고    scopus 로고
    • Global identification of human transcribed sequences with genome tiling arrays
    • Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, et al. (2004) Global identification of human transcribed sequences with genome tiling arrays. Science 306: 2242-2246.
    • (2004) Science , vol.306 , pp. 2242-2246
    • Bertone, P.1    Stolc, V.2    Royce, T.E.3    Rozowsky, J.S.4    Urban, A.E.5
  • 6
    • 10744226888 scopus 로고    scopus 로고
    • Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
    • Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, et al. (2004) Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116: 499-509.
    • (2004) Cell , vol.116 , pp. 499-509
    • Cawley, S.1    Bekiranov, S.2    Ng, H.H.3    Kapranov, P.4    Sekinger, E.A.5
  • 7
    • 0037673675 scopus 로고    scopus 로고
    • Targeting a complex transcriptome: The construction of the mouse full-length cDNA encyclopedia
    • Carninci P, Waki K, Shiraki T, Konno H, Shibata K, et al. (2003) Targeting a complex transcriptome: The construction of the mouse full-length cDNA encyclopedia. Genome Res 13: 1273-1289.
    • (2003) Genome Res , vol.13 , pp. 1273-1289
    • Carninci, P.1    Waki, K.2    Shiraki, T.3    Konno, H.4    Shibata, K.5
  • 8
    • 0033791308 scopus 로고    scopus 로고
    • Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes
    • Carninci P, Shibata Y, Hayatsu N, Sugahara Y, Shibata K, et al. (2000) Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes. Genome Res 10: 1617-1630.
    • (2000) Genome Res , vol.10 , pp. 1617-1630
    • Carninci, P.1    Shibata, Y.2    Hayatsu, N.3    Sugahara, Y.4    Shibata, K.5
  • 9
    • 0035825662 scopus 로고    scopus 로고
    • Functional annotation of a full-length mouse cDNA collection
    • Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, et al. (2001) Functional annotation of a full-length mouse cDNA collection. Nature 409: 685-690.
    • (2001) Nature , vol.409 , pp. 685-690
    • Kawai, J.1    Shinagawa, A.2    Shibata, K.3    Yoshino, M.4    Itoh, M.5
  • 10
    • 0142104045 scopus 로고    scopus 로고
    • Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
    • Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, et al. (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420: 563-573.
    • (2002) Nature , vol.420 , pp. 563-573
    • Okazaki, Y.1    Furuno, M.2    Kasukawa, T.3    Adachi, J.4    Bono, H.5
  • 11
  • 12
    • 24644472515 scopus 로고    scopus 로고
    • Antisense transcription in the mammalian transcriptome
    • Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, et al. (2005) Antisense transcription in the mammalian transcriptome. Science 309: 1564-1566.
    • (2005) Science , vol.309 , pp. 1564-1566
    • Katayama, S.1    Tomaru, Y.2    Kasukawa, T.3    Waki, K.4    Nakanishi, M.5
  • 13
    • 23644460630 scopus 로고    scopus 로고
    • Tag-based approaches for transcriptome research and genome annotation
    • Harbers M, Carninci P (2005) Tag-based approaches for transcriptome research and genome annotation. Nat Methods 2: 495-502.
    • (2005) Nat Methods , vol.2 , pp. 495-502
    • Harbers, M.1    Carninci, P.2
  • 14
    • 9144233601 scopus 로고    scopus 로고
    • Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage
    • U S A
    • Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, et al. (2003) Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci U S A 100: 15776-15781.
    • (2003) Proc Natl Acad Sci , vol.100 , pp. 15776-15781
    • Shiraki, T.1    Kondo, S.2    Katayama, S.3    Waki, K.4    Kasukawa, T.5
  • 15
    • 20844463584 scopus 로고    scopus 로고
    • Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation
    • Ng P, Wei CL, Sung WK, Chiu KP, Lipovich L, et al. (2005) Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat Methods 2: 105-111.
    • (2005) Nat Methods , vol.2 , pp. 105-111
    • Ng, P.1    Wei, C.L.2    Sung, W.K.3    Chiu, K.P.4    Lipovich, L.5
  • 16
    • 0038349624 scopus 로고    scopus 로고
    • Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome
    • Zavolan M, Kondo S, Schonbach C, Adachi J, Hume DA, et al. (2003) Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Res 13: 1290-1300.
    • (2003) Genome Res , vol.13 , pp. 1290-1300
    • Zavolan, M.1    Kondo, S.2    Schonbach, C.3    Adachi, J.4    Hume, D.A.5
  • 17
    • 33646493012 scopus 로고    scopus 로고
    • SPA: A probabilistic algorithm for spliced alignment
    • DOI: 10.1371/journal.pgen.0020024
    • van Nimwegen E, Paul N, Sheridan R, Zavolan M (2006) SPA: A probabilistic algorithm for spliced alignment. PLoS Genet 2: DOI: 10.1371/journal.pgen. 0020024
    • (2006) PLoS Genet , vol.2
    • Van Nimwegen, E.1    Paul, N.2    Sheridan, R.3    Zavolan, M.4
  • 18
    • 33646491292 scopus 로고    scopus 로고
    • A simple physical model predicts small exon length variations
    • DOI: 10.1371/journal.pgen.0020045
    • Chern TM, van Nimwegen E, Kai C, Kawai J, Carninci P, et al. (2006) A simple physical model predicts small exon length variations. PLoS Genet 2: DOI: 10.1371/journal.pgen.0020045
    • (2006) PLoS Genet , vol.2
    • Chern, T.M.1    Van Nimwegen, E.2    Kai, C.3    Kawai, J.4    Carninci, P.5
  • 19
    • 33646466927 scopus 로고    scopus 로고
    • Differential use of signal peptides and membrane domains is a common occurrence in the protein output of transcriptional units
    • DOI: 10.1371/journal.pgen.0020046
    • Davis MJ, Hanson KA, Clark F, Fink JL, Zhang F, et al. (2006) Differential use of signal peptides and membrane domains is a common occurrence in the protein output of transcriptional units. PLoS Genet 2: DOI: 10.1371/journal.pgen.0020046
    • (2006) PLoS Genet , vol.2
    • Davis, M.J.1    Hanson, K.A.2    Clark, F.3    Fink, J.L.4    Zhang, F.5
  • 20
    • 33646480845 scopus 로고    scopus 로고
    • Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases
    • Forrest AR, Taylor DF, Crowe ML, Chalk AM, Waddell NJ, et al. (2006) Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases. Genome Biol 7: R5.
    • (2006) Genome Biol , vol.7
    • Forrest, A.R.1    Taylor, D.F.2    Crowe, M.L.3    Chalk, A.M.4    Waddell, N.J.5
  • 21
    • 33646483032 scopus 로고    scopus 로고
    • The abundance of short proteins in the mammalian proteome
    • DOI: 10.1371/journal.pgen.0020052
    • Frith MC, Forrest AR, Nourbakhsh E, Pang KC, Kai C, et al. (2006) The abundance of short proteins in the mammalian proteome. PLoS Genet 2: DOI: 10.1371/journal.pgen.0020052
    • (2006) PLoS Genet , vol.2
    • Frith, M.C.1    Forrest, A.R.2    Nourbakhsh, E.3    Pang, K.C.4    Kai, C.5
  • 22
    • 0034084035 scopus 로고    scopus 로고
    • Analysis of expressed sequence tags indicates 35,000 human genes
    • Ewing B, Green P (2000) Analysis of expressed sequence tags indicates 35,000 human genes. Nat Genet 25: 232-234.
    • (2000) Nat Genet , vol.25 , pp. 232-234
    • Ewing, B.1    Green, P.2
  • 23
    • 0000508290 scopus 로고    scopus 로고
    • Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence
    • Roest Crollius H, Jaillon O, Bernot A, Dasilva C, Bouneau L, et al. (2000) Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence. Nat Genet 25: 235-238.
    • (2000) Nat Genet , vol.25 , pp. 235-238
    • Roest Crollius, H.1    Jaillon, O.2    Bernot, A.3    Dasilva, C.4    Bouneau, L.5
  • 24
    • 0034204044 scopus 로고    scopus 로고
    • Gene index analysis of the human genome estimates approximately 120,000 genes
    • Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, et al. (2000) Gene index analysis of the human genome estimates approximately 120,000 genes. Nat Genet 25: 239-240.
    • (2000) Nat Genet , vol.25 , pp. 239-240
    • Liang, F.1    Holt, I.2    Pertea, G.3    Karamycheva, S.4    Salzberg, S.L.5
  • 25
    • 33646488342 scopus 로고    scopus 로고
    • Distinguishing protein-coding from non-coding RNAs through support vector machines
    • DOI: 10.1371/journal.pgen.0020029
    • Liu J, Gough J, Rost B (2006) Distinguishing protein-coding from non-coding RNAs through support vector machines. PLoS Genet 2: DOI: 10.1371/journal.pgen.0020029
    • (2006) PLoS Genet , vol.2
    • Liu, J.1    Gough, J.2    Rost, B.3
  • 26
    • 33646474262 scopus 로고    scopus 로고
    • Clusters of internally primed transcripts reveal novel long noncoding RNAs
    • DOI: 10.1371/journal.pgen.0020037
    • Furuno M, Pang KC, Ninomiya N, Fukuda S, Frith MC, et al. (2006) Clusters of internally primed transcripts reveal novel long noncoding RNAs. PLoS Genet 2: DOI: 10.1371/journal.pgen.0020037
    • (2006) PLoS Genet , vol.2
    • Furuno, M.1    Pang, K.C.2    Ninomiya, N.3    Fukuda, S.4    Frith, M.C.5
  • 28
    • 28844443172 scopus 로고    scopus 로고
    • Genome annotation past, present, and future: How to define an ORF at each locus
    • Brent MR (2005) Genome annotation past, present, and future: How to define an ORF at each locus. Genome Res 15: 1777-1786.
    • (2005) Genome Res , vol.15 , pp. 1777-1786
    • Brent, M.R.1
  • 29
    • 1642473033 scopus 로고    scopus 로고
    • Comparative analysis of processed pseudogenes in the mouse and human genomes
    • Zhang Z, Carriero N, Gerstein M (2004) Comparative analysis of processed pseudogenes in the mouse and human genomes. Trends Genet 20: 62-67.
    • (2004) Trends Genet , vol.20 , pp. 62-67
    • Zhang, Z.1    Carriero, N.2    Gerstein, M.3
  • 30
    • 3142594265 scopus 로고    scopus 로고
    • Large-scale analysis of pseudogenes in the human genome
    • Zhang Z, Gerstein M (2004) Large-scale analysis of pseudogenes in the human genome. Curr Opin Genet Dev 14: 328-335.
    • (2004) Curr Opin Genet Dev , vol.14 , pp. 328-335
    • Zhang, Z.1    Gerstein, M.2
  • 31
    • 0038414560 scopus 로고    scopus 로고
    • An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene
    • Hirotsune S, Yoshida N, Chen A, Garrett L, Sugiyama F, et al. (2003) An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature 423: 91-96.
    • (2003) Nature , vol.423 , pp. 91-96
    • Hirotsune, S.1    Yoshida, N.2    Chen, A.3    Garrett, L.4    Sugiyama, F.5
  • 32
    • 33646468946 scopus 로고    scopus 로고
    • Pseudo-messenger RNA: Phantoms of the transcriptome
    • DOI: 10.1371/journal.pgen.0020023
    • Frith MC, Wilming LG, Forrest A, Kawaji H, Tan SL, et al. (2006) Pseudo-messenger RNA: Phantoms of the transcriptome. PLoS Genet 2: DOI: 10.1371/journal.pgen.0020023
    • (2006) PLoS Genet , vol.2
    • Frith, M.C.1    Wilming, L.G.2    Forrest, A.3    Kawaji, H.4    Tan, S.L.5
  • 33
    • 0346155809 scopus 로고    scopus 로고
    • Pseudogenes: Are they "junk" or functional DNA?
    • Balakirev ES, Ayala FJ (2003) Pseudogenes: Are they "junk" or functional DNA? Annu Rev Genet 37: 123-151.
    • (2003) Annu Rev Genet , vol.37 , pp. 123-151
    • Balakirev, E.S.1    Ayala, F.J.2
  • 34
    • 0141867857 scopus 로고    scopus 로고
    • Challenging the dogma: The hidden layer of non-protein-coding RNAs in complex organisms
    • Mattick JS (2003) Challenging the dogma: The hidden layer of non-protein-coding RNAs in complex organisms. Bioessays 25: 930-939.
    • (2003) Bioessays , vol.25 , pp. 930-939
    • Mattick, J.S.1
  • 35
    • 29444455072 scopus 로고    scopus 로고
    • A mouse atlas of gene expression: Large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells
    • U S A
    • Siddiqui AS, Khattra J, Delaney AD, Zhao Y, Astell C, et al. (2005) 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 U S A 102: 18485-18490.
    • (2005) Proc Natl Acad Sci , vol.102 , pp. 18485-18490
    • Siddiqui, A.S.1    Khattra, J.2    Delaney, A.D.3    Zhao, Y.4    Astell, C.5
  • 36
    • 33646484360 scopus 로고    scopus 로고
    • A method for similarity search of genomic positional expression using CAGE
    • DOI: 10.1371/journal.pgen.0020044
    • Seno S, Takenaka Y, Kai C, Kawai J, Carninci P, et al. (2006) A method for similarity search of genomic positional expression using CAGE. PLoS Genet 2: DOI: 10.1371/journal.pgen.0020044
    • (2006) PLoS Genet , vol.2
    • Seno, S.1    Takenaka, Y.2    Kai, C.3    Kawai, J.4    Carninci, P.5
  • 37
  • 38
    • 33646493110 scopus 로고    scopus 로고
    • Genome-wide analysis of mammalian promoter architecture and evolution based upon human and mouse CAGE data
    • In press
    • Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa S, et al. (2006) Genome-wide analysis of mammalian promoter architecture and evolution based upon human and mouse CAGE data. Nat Genet: In press.
    • (2006) Nat Genet
    • Carninci, P.1    Sandelin, A.2    Lenhard, B.3    Katayama, S.4    Shimokawa, S.5
  • 39
    • 20144386500 scopus 로고    scopus 로고
    • Large-scale collection and characterization of promoters of human and mouse genes
    • Suzuki Y, Yamashita R, Shirota M, Sakakibara Y, Chiba J, et al. (2004) Large-scale collection and characterization of promoters of human and mouse genes. In Silico Biol 4: 429-444.
    • (2004) Silico Biol , vol.4 , pp. 429-444
    • Suzuki, Y.1    Yamashita, R.2    Shirota, M.3    Sakakibara, Y.4    Chiba, J.5
  • 42
    • 33646489947 scopus 로고    scopus 로고
    • Heterotachy in mammalian promoter evolution
    • DOI: 10.1371/journal.pgen.0020030
    • Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, et al. (2006) Heterotachy in mammalian promoter evolution. PLoS Genet 2: DOI: 10.1371/journal.pgen.0020030
    • (2006) PLoS Genet , vol.2
    • Taylor, M.S.1    Kai, C.2    Kawai, J.3    Carninci, P.4    Hayashizaki, Y.5
  • 43
    • 24044455869 scopus 로고    scopus 로고
    • Genome sequencing in microfabricated high-density picolitre reactors
    • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
    • (2005) Nature , vol.437 , pp. 376-380
    • Margulies, M.1    Egholm, M.2    Altman, W.E.3    Attiya, S.4    Bader, J.S.5
  • 44
    • 7444260846 scopus 로고    scopus 로고
    • The ENCODE (ENCyclopedia of DNA Elements) Project
    • ENCODE Project Consortium (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306: 636-640.
    • (2004) Science , vol.306 , pp. 636-640
  • 45
    • 33646490270 scopus 로고    scopus 로고
    • Transcript annotation in FANTOM3: Mouse gene catalog based on physical cDNAs
    • DOI: 10.1371/journal.pgen.0020062
    • Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, et al. (2006) Transcript annotation in FANTOM3: Mouse gene catalog based on physical cDNAs. PLoS Genet 2: DOI: 10.1371/journal.pgen.0020062
    • (2006) PLoS Genet , vol.2
    • Maeda, N.1    Kasukawa, T.2    Oyama, R.3    Gough, J.4    Frith, M.5
  • 47
    • 33644874143 scopus 로고    scopus 로고
    • CAGE Basic/Analysis Databases: The CAGE resource for comprehensive promoter analysis
    • Kawaji H, Kasukawa T, Fukuda S, Katayama S, Kai C, et al. (2006) CAGE Basic/Analysis Databases: The CAGE resource for comprehensive promoter analysis. Nucleic Acids Res 34: D632-D636.
    • (2006) Nucleic Acids Res , vol.34
    • Kawaji, H.1    Kasukawa, T.2    Fukuda, S.3    Katayama, S.4    Kai, C.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.