PlantRGS: A web server for the identification of most suitable candidate reference genes for quantitative gene expression studies in plants

DNA Research

Volumn 18, Issue 6, 2011, Pages 463-470

  Patel, Ravi K ^a   Jain, Mukesh ^a  

^a NATIONAL INSTITUTE OF PLANT GENOME RESEARCH   (India)

Author keywords

gene expression; microarray; normalization; reference gene; web server

Indexed keywords

ARTICLE; COMPUTER INTERFACE; GENE EXPRESSION; GENE IDENTIFICATION; GENOME; META ANALYSIS (TOPIC); MICROARRAY ANALYSIS; NONHUMAN; PLANT GENE; QUANTITATIVE ANALYSIS;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; INTERNET; PLANTS; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 82255186884     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dsr032     Document Type: Article

References (24)

1. Clarke, J.D. and Zhu, T. 2006, Microarray analysis of the transcriptome as a stepping stone towards understanding biological systems: practical considerations and perspectives, Plant J., 45, 630-50. (Pubitemid 43373713)
2. Czechowski, T., Bari, R.P., Stitt, M., Scheible, W.R. and Udvardi, M.K. 2004, Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root-and shoot-specific genes, Plant J., 38, 366-79. (Pubitemid 38503736)
3. Gachon, C., Mingam, A. and Charrier, B. 2004, Real-time PCR: what relevance to plant studies?, J. Exp. Bot., 55, 1445-54. (Pubitemid 38940856)
4. Garg, R., Jhanwar, S., Tyagi, A.K. and Jain, M. 2010, Genome-wide survey and expression analysis suggest diverse roles of glutaredoxin gene family members during development and response to various stimuli in rice, DNA Res., 17, 353-67.
5. Nolan, T., Hands, R.E. and Bustin, S.A. 2006, Quantification of mRNA using real-time RT-PCR, Nat. Protoc., 1, 1559-82.
6. Thellin, O., Zorzi, W., Lakaye, B., et al. 1999, Housekeeping genes as internal standards: use and limits, J. Biotechnol., 75, 291-5. (Pubitemid 29486627)
7. Schmittgen, T.D. and Zakrajsek, B.A. 2000, Effect of experimental treatment on housekeeping gene expression: validation by real-time, quantitative RT-PCR, J. Biochem. Biophys. Methods, 46, 69-81.
8. Lee, P.D., Sladek, R., Greenwood, C.M. and Hudson, T.J. 2002, Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies, Genome Res., 12, 292-7. (Pubitemid 34162995)
9. Czechowski, T., Stitt, M., Altmann, T., Udvardi, M.K. and Scheible, W.R. 2005, Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis, Plant Physiol., 139, 5-17. (Pubitemid 43951587)
10. Rubie, C., Kempf, K., Hans, J., et al. 2005, Housekeeping gene variability in normal and cancerous colorectal, pancreatic, esophageal, gastric and hepatic tissues, Mol. Cell. Probes, 19, 101-9. (Pubitemid 40174728)
11. Gutierrez, L., Mauriat, M., Guenin, S., et al. 2008, The lack of a systematic validation of reference genes: a serious pitfall undervalued in reverse transcription-polymerase chain reaction (RT-PCR) analysis in plants, Plant Biotechnol. J., 6, 609-18. (Pubitemid 351989484)
12. Nicot, N., Hausman, J.F., Hoffmann, L. and Evers, D. 2005, Housekeeping gene selection for real-time RTPCR normalization in potato during biotic and abiotic stress, J. Exp. Bot., 56, 2907-14. (Pubitemid 41507227)
13. Jain, M., Nijhawan, A., Tyagi, A.K. and Khurana, J.P. 2006, Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative realtime PCR, Biochem. Biophys. Res. Commun., 345, 646-51. (Pubitemid 43776982)
14. Remans, T., Smeets, K., Opdenakker, K., Mathijsen, D., Vangronsveld, J. and Cuypers, A. 2008, Normalisation of real-time RT-PCR gene expression measurements in Arabidopsis thaliana exposed to increased metal concentrations, Planta, 227, 1343-9.
15. Garg, R., Sahoo, A., Tyagi, A.K. and Jain, M. 2010, Validation of internal control genes for quantitative gene expression studies in chickpea (Cicer arietinum L.), Biochem. Biophys. Res. Commun., 396, 283-8.
16. Libault, M., Thibivilliers, S., Bilgin, D.D., et al. 2008, Identification of four soybean reference genes for gene expression normalization, Plant Genome, 1, 44-54.
17. Jain, M. 2009, Genome-wide identification of novel internal control genes for normalization of gene expression during various stages of development in rice, Plant Sci., 176, 702-6.
18. Kwon, M.J., Oh, E., Lee, S., et al. 2009, Identification of novel reference genes using multiplatform expression data and their validation for quantitative gene expression analysis, PLoS One, 4, e6162.
19. Narsai, R., Ivanova, A., Ng, S. and Whelan, J. 2010, Defining reference genes in Oryza sativa using organ, development, biotic and abiotic transcriptome datasets, BMC Plant Biol., 10, 56.
20. Vandesompele, J., De Preter, K., Pattyn, F., et al. 2002, Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes, Genome Biol., 3, RESEARCH0034.
21. Wise, R.P., Caldo, R.A., Hong, L., Shen, L., Cannon, E. and Dickerson, J.A. 2007, BarleyBase/PLEXdb: a unified expression profiling database for plants and plant pathogens, Methods Mol. Biol., 406, 347-63. (Pubitemid 351367182)
22. Bullard, J.H., Purdom, E., Hansen, K.D. and Dudoit, S. 2010, Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments, BMC Bioinformatics, 11, 94.
23. Coker, J.S. and Davies, E. 2003, Selection of candidate housekeeping controls in tomato plants using EST data, Biotechniques, 35, 740-8. (Pubitemid 37248358)
24. Chari, R., Lonergan, K.M., Pikor, L.A., et al. 2010, A sequence-based approach to identify reference genes for gene expression analysis, BMC Med. Genomics, 3, 32.