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Volumn 41, Issue D1, 2013, Pages

The Rice Genome Knowledgebase (RGKbase): An annotation database for rice comparative genomics and evolutionary biology

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TRANSCRIPTOME;

EID: 84876524472     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1225     Document Type: Article
Times cited : (28)

References (69)
  • 4
    • 84907150192 scopus 로고    scopus 로고
    • The map-based sequence of the rice genome
    • International Rice Genome Sequencing Project
    • International Rice Genome Sequencing Project. (2005) The map-based sequence of the rice genome. Nature, 436, 793-800.
    • (2005) Nature , vol.436 , pp. 793-800
  • 6
    • 84655176647 scopus 로고    scopus 로고
    • Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm
    • Huang, X., Zhao, Y., Wei, X., Li, C., Wang, A., Zhao, Q., Li, W., Guo, Y., Deng, L., Zhu, C. et al. (2011) Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat. Genet., 44, 32-39.
    • (2011) Nat. Genet. , vol.44 , pp. 32-39
    • Huang, X.1    Zhao, Y.2    Wei, X.3    Li, C.4    Wang, A.5    Zhao, Q.6    Li, W.7    Guo, Y.8    Deng, L.9    Zhu, C.10
  • 7
    • 9144231248 scopus 로고    scopus 로고
    • BGI-RIS: An integrated information resource and comparative analysis workbench for rice genomics
    • Zhao, W., Wang, J., He, X., Huang, X., Jiao, Y., Dai, M., Wei, S., Fu, J., Chen, Y., Ren, X. et al. (2004) BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. Nucleic Acids Res., 32, D377-D382.
    • (2004) Nucleic Acids Res. , vol.32
    • Zhao, W.1    Wang, J.2    He, X.3    Huang, X.4    Jiao, Y.5    Dai, M.6    Wei, S.7    Fu, J.8    Chen, Y.9    Ren, X.10
  • 10
    • 33750488136 scopus 로고    scopus 로고
    • Heterosis and polymorphisms of gene expression in an elite rice hybrid as revealed by a microarray analysis of 9198 unique ESTs
    • Huang, Y., Zhang, L., Zhang, J., Yuan, D., Xu, C., Li, X., Zhou, D., Wang, S. and Zhang, Q. (2006) Heterosis and polymorphisms of gene expression in an elite rice hybrid as revealed by a microarray analysis of 9198 unique ESTs. Plant Mol. Biol., 62, 579-591.
    • (2006) Plant Mol. Biol. , vol.62 , pp. 579-591
    • Huang, Y.1    Zhang, L.2    Zhang, J.3    Yuan, D.4    Xu, C.5    Li, X.6    Zhou, D.7    Wang, S.8    Zhang, Q.9
  • 11
    • 0035142211 scopus 로고    scopus 로고
    • Survey of transposable elements from rice genomic sequences
    • Turcotte, K., Srinivasan, S. and Bureau, T. (2001) Survey of transposable elements from rice genomic sequences. Plant J., 25, 169-179.
    • (2001) Plant J. , vol.25 , pp. 169-179
    • Turcotte, K.1    Srinivasan, S.2    Bureau, T.3
  • 13
    • 34547592867 scopus 로고    scopus 로고
    • LTR-FINDER: An efficient tool for the prediction of full-length LTR retrotransposons
    • Xu, Z. and Wang, H. (2007) LTR-FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res., 35, W265-W268.
    • (2007) Nucleic Acids Res. , vol.35
    • Xu, Z.1    Wang, H.2
  • 14
    • 0037433054 scopus 로고    scopus 로고
    • LTR-STRUC: A novel search and identification program for LTR retrotransposons
    • McCarthy, E.M. and McDonald, J.F. (2003) LTR-STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics, 19, 362-367.
    • (2003) Bioinformatics , vol.19 , pp. 362-367
    • McCarthy, E.M.1    McDonald, J.F.2
  • 15
    • 39749179047 scopus 로고    scopus 로고
    • LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons
    • Ellinghaus, D., Kurtz, S. and Willhoeft, U. (2008) LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics, 9, 18.
    • (2008) BMC Bioinformatics , vol.9 , pp. 18
    • Ellinghaus, D.1    Kurtz, S.2    Willhoeft, U.3
  • 16
    • 78650432054 scopus 로고    scopus 로고
    • MITE-Hunter: A program for discovering miniature inverted-repeat transposable elements from genomic sequences
    • Han, Y. and Wessler, S.R. (2010) MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences. Nucleic Acids Res., 38, e199.
    • (2010) Nucleic Acids Res. , vol.38
    • Han, Y.1    Wessler, S.R.2
  • 17
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: A program to analyze DNA sequences
    • Benson, G. (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res., 27, 573-580.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 573-580
    • Benson, G.1
  • 18
    • 34547852208 scopus 로고    scopus 로고
    • SciRoKo: A new tool for whole genome microsatellite search and investigation
    • Kofler, R., Schlotterer, C. and Lelley, T. (2007) SciRoKo: a new tool for whole genome microsatellite search and investigation. Bioinformatics, 23, 1683-1685.
    • (2007) Bioinformatics , vol.23 , pp. 1683-1685
    • Kofler, R.1    Schlotterer, C.2    Lelley, T.3
  • 19
    • 4344700574 scopus 로고    scopus 로고
    • Isochore structures in the genome of the plant Arabidopsis thaliana
    • Zhang, R. and Zhang, C.T. (2004) Isochore structures in the genome of the plant Arabidopsis thaliana. J. Mol. Evol., 59, 227-238.
    • (2004) J. Mol. Evol. , vol.59 , pp. 227-238
    • Zhang, R.1    Zhang, C.T.2
  • 21
    • 33747858422 scopus 로고    scopus 로고
    • GC-Profile: A web-based tool for visualizing and analyzing the variation of GC content in genomic sequences
    • Gao, F. and Zhang, C.T. (2006) GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences. Nucleic Acids Res., 34, W686-W691.
    • (2006) Nucleic Acids Res. , vol.34
    • Gao, F.1    Zhang, C.T.2
  • 23
    • 39049168212 scopus 로고    scopus 로고
    • Generic eukaryotic core promoter prediction using structural features of DNA
    • Abeel, T., Saeys, Y., Bonnet, E., Rouze, P. and Van de Peer, Y. (2008) Generic eukaryotic core promoter prediction using structural features of DNA. Genome Res., 18, 310-323.
    • (2008) Genome Res. , vol.18 , pp. 310-323
    • Abeel, T.1    Saeys, Y.2    Bonnet, E.3    Rouze, P.4    Van De Peer, Y.5
  • 25
    • 84859436530 scopus 로고    scopus 로고
    • NCBI Reference Sequences (RefSeq): Current status, new features and genome annotation policy
    • Pruitt, K.D., Tatusova, T., Brown, G.R. and Maglott, D.R. (2012) NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res., 40, D130-D135.
    • (2012) Nucleic Acids Res. , vol.40
    • Pruitt, K.D.1    Tatusova, T.2    Brown, G.R.3    Maglott, D.R.4
  • 26
    • 84860833500 scopus 로고    scopus 로고
    • Reorganizing the protein space at the Universal Protein Resource (UniProt)
    • The UniProt Consortium
    • The UniProt Consortium. (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res., 40, D71-D75.
    • (2012) Nucleic Acids Res. , vol.40
  • 27
    • 2942544417 scopus 로고    scopus 로고
    • Gene finding in novel genomes
    • Korf, I. (2004) Gene finding in novel genomes. BMC Bioinformatics, 5, 59.
    • (2004) BMC Bioinformatics , vol.5 , pp. 59
    • Korf, I.1
  • 28
    • 43349093149 scopus 로고    scopus 로고
    • Using N-SCAN or TWINSCAN to predict gene structures in genomic DNA sequences
    • Chapter 4, Unit 4.8
    • van Baren, M.J., Koebbe, B.C. and Brent, M.R. (2007) Using N-SCAN or TWINSCAN to predict gene structures in genomic DNA sequences. Curr. Protoc. Bioinformatics, Chapter 4, Unit 4.8.
    • (2007) Curr. Protoc. Bioinformatics
    • Van Baren, M.J.1    Koebbe, B.C.2    Brent, M.R.3
  • 30
    • 84858983547 scopus 로고    scopus 로고
    • KEGG for integration and interpretation of large-scale molecular data sets
    • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. and Tanabe, M. (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res., 40, D109-D114.
    • (2012) Nucleic Acids Res. , vol.40
    • Kanehisa, M.1    Goto, S.2    Sato, Y.3    Furumichi, M.4    Tanabe, M.5
  • 32
    • 78651337578 scopus 로고    scopus 로고
    • PlantTFDB 2.0: Update and improvement of the comprehensive plant transcription factor database
    • Zhang, H., Jin, J., Tang, L., Zhao, Y., Gu, X., Gao, G. and Luo, J. (2011) PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database. Nucleic Acids Res., 39, D1114-D1117.
    • (2011) Nucleic Acids Res. , vol.39
    • Zhang, H.1    Jin, J.2    Tang, L.3    Zhao, Y.4    Gu, X.5    Gao, G.6    Luo, J.7
  • 34
    • 0030854739 scopus 로고    scopus 로고
    • TRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • Lowe, T.M. and Eddy, S.R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 36
    • 38449092636 scopus 로고    scopus 로고
    • SnoReport: Computational identification of snoRNAs with unknown targets
    • Hertel, J., Hofacker, I.L. and Stadler, P.F. (2008) SnoReport: computational identification of snoRNAs with unknown targets. Bioinformatics, 24, 158-164.
    • (2008) Bioinformatics , vol.24 , pp. 158-164
    • Hertel, J.1    Hofacker, I.L.2    Stadler, P.F.3
  • 37
    • 0027249595 scopus 로고
    • DbEST - Database for "expressed sequence tags"
    • Boguski, M.S., Lowe, T.M. and Tolstoshev, C.M. (1993) dbEST - database for "expressed sequence tags". Nat. Genet., 4, 332-333.
    • (1993) Nat. Genet. , vol.4 , pp. 332-333
    • Boguski, M.S.1    Lowe, T.M.2    Tolstoshev, C.M.3
  • 38
    • 78651293534 scopus 로고    scopus 로고
    • MiRBase: Integrating microRNA annotation and deep-sequencing data
    • Kozomara, A. and Griffiths-Jones, S. (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res., 39, D152-D157.
    • (2011) Nucleic Acids Res. , vol.39
    • Kozomara, A.1    Griffiths-Jones, S.2
  • 41
    • 77951871117 scopus 로고    scopus 로고
    • Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome
    • Zhang, G., Guo, G., Hu, X., Zhang, Y., Li, Q., Li, R., Zhuang, R., Lu, Z., He, Z., Fang, X. et al. (2010) Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res., 20, 646-654.
    • (2010) Genome Res. , vol.20 , pp. 646-654
    • Zhang, G.1    Guo, G.2    Hu, X.3    Zhang, Y.4    Li, Q.5    Li, R.6    Zhuang, R.7    Lu, Z.8    He, Z.9    Fang, X.10
  • 42
    • 84858047784 scopus 로고    scopus 로고
    • Transcriptome analysis of rice mature root tissue and root tips in early development by massive parallel sequencing
    • Kyndt, T., Denil, S., Haegeman, A., Trooskens, G., De Meyer, T., Van Criekinge, W. and Gheysen, G. (2012) Transcriptome analysis of rice mature root tissue and root tips in early development by massive parallel sequencing. J. Exp. Bot., 63, 2141-2157.
    • (2012) J. Exp. Bot. , vol.63 , pp. 2141-2157
    • Kyndt, T.1    Denil, S.2    Haegeman, A.3    Trooskens, G.4    De Meyer, T.5    Van Criekinge, W.6    Gheysen, G.7
  • 44
    • 77950346035 scopus 로고    scopus 로고
    • Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids
    • He, G., Zhu, X., Elling, A.A., Chen, L., Wang, X., Guo, L., Liang, M., He, H., Zhang, H., Chen, F. et al. (2010) Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell, 22, 17-33.
    • (2010) Plant Cell , vol.22 , pp. 17-33
    • He, G.1    Zhu, X.2    Elling, A.A.3    Chen, L.4    Wang, X.5    Guo, L.6    Liang, M.7    He, H.8    Zhang, H.9    Chen, F.10
  • 45
    • 79953837880 scopus 로고    scopus 로고
    • OryzaPG-DB: Rice proteome database based on shotgun proteogenomics
    • Helmy, M., Tomita, M. and Ishihama, Y. (2011) OryzaPG-DB: rice proteome database based on shotgun proteogenomics. BMC Plant Biol., 11, 63.
    • (2011) BMC Plant Biol. , vol.11 , pp. 63
    • Helmy, M.1    Tomita, M.2    Ishihama, Y.3
  • 46
    • 55849143642 scopus 로고    scopus 로고
    • Proteomic profiling of rice embryos from a hybrid rice cultivar and its parental lines
    • Wang, W., Meng, B., Ge, X., Song, S., Yang, Y., Yu, X., Wang, L., Hu, S., Liu, S. and Yu, J. (2008) Proteomic profiling of rice embryos from a hybrid rice cultivar and its parental lines. Proteomics, 8, 4808-4821.
    • (2008) Proteomics , vol.8 , pp. 4808-4821
    • Wang, W.1    Meng, B.2    Ge, X.3    Song, S.4    Yang, Y.5    Yu, X.6    Wang, L.7    Hu, S.8    Liu, S.9    Yu, J.10
  • 47
    • 84862936211 scopus 로고    scopus 로고
    • Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes
    • Xu, X., Liu, X., Ge, S., Jensen, J.D., Hu, F., Li, X., Dong, Y., Gutenkunst, R.N., Fang, L., Huang, L. et al. (2011) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat. Biotechnol., 30, 105-111.
    • (2011) Nat. Biotechnol. , vol.30 , pp. 105-111
    • Xu, X.1    Liu, X.2    Ge, S.3    Jensen, J.D.4    Hu, F.5    Li, X.6    Dong, Y.7    Gutenkunst, R.N.8    Fang, L.9    Huang, L.10
  • 50
    • 4143051590 scopus 로고    scopus 로고
    • Ancestral genome duplication in rice
    • Guyot, R. and Keller, B. (2004) Ancestral genome duplication in rice. Genome, 47, 610-614.
    • (2004) Genome , vol.47 , pp. 610-614
    • Guyot, R.1    Keller, B.2
  • 51
    • 54949108148 scopus 로고    scopus 로고
    • Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
    • Paten, B., Herrero, J., Beal, K., Fitzgerald, S. and Birney, E. (2008) Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res., 18, 1814-1828.
    • (2008) Genome Res. , vol.18 , pp. 1814-1828
    • Paten, B.1    Herrero, J.2    Beal, K.3    Fitzgerald, S.4    Birney, E.5
  • 52
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • Enright, A.J., Van Dongen, S. and Ouzounis, C.A. (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res., 30, 1575-1584.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 53
  • 54
    • 77951682635 scopus 로고    scopus 로고
    • KaKs-Calculator 2.0: A toolkit incorporating gamma-series methods and sliding window strategies
    • Wang, D., Zhang, Y., Zhang, Z., Zhu, J. and Yu, J. (2010) KaKs-Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics Proteomics Bioinformatics, 8, 77-80.
    • (2010) Genomics Proteomics Bioinformatics , vol.8 , pp. 77-80
    • Wang, D.1    Zhang, Y.2    Zhang, Z.3    Zhu, J.4    Yu, J.5
  • 55
    • 79951788396 scopus 로고    scopus 로고
    • Nonsynonymous substitution rate (Ka) is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genes
    • Wang, D., Liu, F., Wang, L., Huang, S. and Yu, J. (2011) Nonsynonymous substitution rate (Ka) is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genes. Biol. Direct, 6, 13.
    • (2011) Biol. Direct , vol.6 , pp. 13
    • Wang, D.1    Liu, F.2    Wang, L.3    Huang, S.4    Yu, J.5
  • 57
    • 0036226603 scopus 로고    scopus 로고
    • BLAT - The BLAST-like alignment tool
    • Kent, W.J. (2002) BLAT - the BLAST-like alignment tool. Genome Res., 12, 656-664.
    • (2002) Genome Res. , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 58
    • 43349098495 scopus 로고    scopus 로고
    • Using the Generic Genome Browser (GBrowse)
    • Chapter 9, Unit 9.9
    • Donlin, M.J. (2007) Using the Generic Genome Browser (GBrowse). Curr. Protoc. Bioinformatics, Chapter 9, Unit 9.9.
    • (2007) Curr. Protoc. Bioinformatics
    • Donlin, M.J.1
  • 61
    • 10744220149 scopus 로고    scopus 로고
    • A unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales
    • Kuhl, J.C., Cheung, F., Yuan, Q., Martin, W., Zewdie, Y., McCallum, J., Catanach, A., Rutherford, P., Sink, K.C., Jenderek, M. et al. (2004) A unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales. Plant Cell, 16, 114-125.
    • (2004) Plant Cell , vol.16 , pp. 114-125
    • Kuhl, J.C.1    Cheung, F.2    Yuan, Q.3    Martin, W.4    Zewdie, Y.5    McCallum, J.6    Catanach, A.7    Rutherford, P.8    Sink, K.C.9    Jenderek, M.10
  • 62
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 63
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 64
    • 84859699831 scopus 로고    scopus 로고
    • The gene ontology: Enhancements for 2011
    • The Gene Ontology Consortium
    • The Gene Ontology Consortium. (2012) The Gene Ontology: enhancements for 2011. Nucleic Acids Res., 40, D559-D564.
    • (2012) Nucleic Acids Res. , vol.40
  • 65
    • 83455221626 scopus 로고    scopus 로고
    • LCGbase: A comprehensive database for lineage-based co-regulated genes
    • Wang, D., Zhang, Y., Fan, Z., Liu, G. and Yu, J. (2012) LCGbase: a comprehensive database for lineage-based co-regulated genes. Evol. Bioinform. Online, 8, 39-46.
    • (2012) Evol. Bioinform. Online , vol.8 , pp. 39-46
    • Wang, D.1    Zhang, Y.2    Fan, Z.3    Liu, G.4    Yu, J.5


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