RiceSRTFDB: A database of rice transcription factors containing comprehensive expression, cis-regulatory element and mutant information to facilitate gene function analysis

Database

Volumn 2013, Issue , 2013, Pages

  Priya, Pushp ^a   Jain, Mukesh ^a  

^a NATIONAL INSTITUTE OF PLANT GENOME RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR; VEGETABLE PROTEIN;

ARTICLE; DROUGHT; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; INTERNET; METABOLISM; MUTATION; PHYSIOLOGICAL STRESS; PLANT GENE; REGULATORY SEQUENCE; RICE; SALINITY;

DATABASES, GENETIC; DROUGHTS; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; INTERNET; MUTATION; ORYZA SATIVA; PLANT PROTEINS; REGULATORY SEQUENCES, NUCLEIC ACID; SALINITY; STRESS, PHYSIOLOGICAL; TRANSCRIPTION FACTORS;

EID: 84885907112     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bat027     Document Type: Article

References (38)

1. Hirayama,T. and Shinozaki,K. (2010) Research on plant abiotic stress responses in the post-genome era: past, present and future. Plant J., 61, 1041-1052.
2. Hadiarto,T. and Tran,L.S. (2011) Progress studies of drought-responsive genes in rice. Plant Cell Rep., 30, 297-310.
3. Cooper,B., Clarke,J.D., Budworth,P. et al. (2003) A network of rice genes associated with stress response and seed development. Proc. Natl. Acad. Sci. USA, 100, 4945-4950.
4. Rabbani,M.A., Maruyama,K., Abe,H. et al. (2003) Monitoring expression profiles of rice genes under cold, drought, and highsalinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses. Plant Physiol., 133, 1755-1767.
5. Lan,L., Li,M., Lai,Y. et al. (2005) Microarray analysis reveals similarities and variations in genetic programs controlling pollination/ fertilization and stress responses in rice (Oryza sativa L.). Plant Mol. Biol., 59, 151-164.
6. Zhou,J., Wang,X., Jiao,Y. et al. (2007) Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf and panicle. Plant Mol. Biol., 63, 591-608.
7. Ray,S., Dasana,P.K., Giri,J. et al. (2011) Modulation of transcription factor and metabolic pathway genes in response to water-deficit stress in rice. Funct. Integr. Genomics, 11, 157-178.
8. Nakashima,K., Ito,Y. and Yamaguchi-Shinozaki,K. (2009) Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses. Plant Physiol., 149, 88-95.
9. Urano,K., Kurihara,Y., Seki,M. et al. (2010) 'Omics' analyses of regulatory networks in plant abiotic stress responses. Curr. Opin. Plant Biol., 13, 1-7.
10. Yang,S., Vanderbeld,B., Wan,J. et al. (2010) Narrowing down the targets: towards successful genetic engineering of drought-tolerant crops. Mol. Plant, 3, 469-490.
11. Golldack,D., Lu'king,I. and Yang,O. (2011) Plant tolerance to drought and salinity: stress regulating transcription factors and their functional significance in the cellular transcriptional network. Plant Cell Rep., 30, 1383-1391.
12. Balaji,J., Crouch,J.H., Petite,P.V.N.S. et al. (2006) A database of annotated tentative orthologs from crop abiotic stress transcripts. Bioinformation, 1, 225-227.
13. Prabha,R., Ghosh,I. and Singh,D.P. (2011) Plant Stress Gene Database: A collection of plant genes responding to stress condition. ARPN J. Sci. Technol., 1, 28-31.
14. Shameer,K., Ambika,S., Varghese,S.M. et al. (2009) STIFDBArabidopsis stress responsive transcription factor database. Int. J. Plant Genomics, 2009, 583429.
15. Smita,S., Lenka,S.K., Katiyar,A. et al. (2011) QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice. Database, 2011, bar037.
16. Miyao,A., Iwasaki,Y., Kitano,H. et al. (2007) A large-scale collection of phenotypic data describing an insertional mutant population to facilitate functional analysis of rice genes. Plant Mol. Biol., 63, 625-635.
17. Mochida,K. and Shinozaki,K. (2010) Genomics and bioinformatics resources for crop improvement. Plant Cell Physiol., 51, 497-523.
18. Hamada,K., Hongo,K., Suwabe,K. et al. (2011) OryzaExpress: an integrated database of gene expression networks and omics annotations in rice. Plant Cell Physiol., 52, 220-229.
19. Nagamura,Y., Antonio,B.A., Sato,Y. et al. (2011) Rice TOGO Browser: a platform to retrieve integrated information on rice functional and applied genomics. Plant Cell Physiol., 52, 230-237.
20. Gao,G., Shong,Y., Guo,A. et al. (2006) DRTF: a datbase of rice transcription factors. Bioinformatics, 22, 1286-1287.
21. Perez-Rodriguez,P., Riano-Pachon,D.M., Correa,L.G.G. et al. (2010) PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res., 38, D822-D827.
22. Ouyang,S., Zhu,W., Hamilton,J. et al. (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res., 35, D883-D887.
23. Sakai,H., Lee,S.S., Tanaka,T. et al. (2013) Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Plant Cell Physiol., 54, e6.
24. Rensink,W.A. and Buell,C.R. (2005) Microarray expression profiling resources for plant genomics. Trends Plant Sci., 10, 603-609.
25. Jain,M., Nijhawan,A., Arora,R. et al. (2007) F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol., 143, 1467-1483.
26. Walia,H., Wilson,C., Ismail,A.M. et al. (2009) Comparing genomic expression patterns across plant species reveals highly diverged transcriptional dynamics in response to salt stress. BMC Genomics, 10, 398.
27. Cotsaftis,O., Plett,D., Johnson,A.A. et al. (2011) Root-specific transcript profiling of contrasting rice genotypes in response to salinity stress. Mol. Plant, 4, 25-41.
28. Wang,D., Pan,Y., Zhao,X. et al. (2011) Genome-wide temporal-spatial gene expression profiling of drought responsiveness in rice. BMC Genomics, 12, 149.
29. Jain,M., Tyagi,A.K. and Khurana,J.P. (2008) Genome-wide identification, classification, evolutionary expansion and expression analyses of homeobox genes in rice. FEBS J., 275, 2845-2861.
30. Jain,M. and Khurana,J.P. (2009) Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice. FEBS J., 276, 3148-3162.
31. Nuruzzaman,M., Manimekalai,R., Sharoni,A.M. et al. (2010) Genome-wide analysis of NAC transcription factor family in rice. Gene, 465, 30-44.
32. Hakim,M.A., Juraimi,A.S., Begum,M. et al. (2010) Effect of salt stress on germination and early seedling growth of rice (Oryza sativa L.). Afr. J. Biotechnol., 9, 1911-1918.
33. Chen,W., Provart,N.J., Glazebrook,J. et al. (2002) Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses. Plant Cell, 14, 559-574.
34. Miyao,A., Tanaka,K., Murata,K. et al. (2003) Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell, 15, 1771-1780.
35. Ohmori,S., Kimizu,M., Sugita,M. et al. (2009) MOSAIC FLORAL ORGANS1, an AGL6-like MADS box gene, regulates floral organ identity and meristem fate in rice. Plant Cell, 21, 3008-3025.
36. Kishi-Kaboshi,M., Okada,K., Kurimoto,L. et al. (2010) A rice fungal MAMP-responsive MAPK cascade regulates metabolic flow to antimicrobial metabolite synthesis. Plant J., 63, 599-612.
37. Sugimoto,K., Takeuchi,Y., Ebana,K. et al. (2010) Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice. Proc. Natl. Acad. Sci. USA, 107, 5792-5797.
38. Yoshii,M., Yamazaki,M., Rakwal,R. et al. (2010) The NAC transcription factor RIM1 of rice is a new regulator of jasmonate signaling. Plant J., 61, 804-815.