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Volumn 63, Issue 5, 2007, Pages 679-688

A combined strategy of "in silico" transcriptome analysis and web search engine optimization allows an agile identification of reference genes suitable for normalization in gene expression studies

Author keywords

"In silico" analysis; Literature search; Reference genes; RNA quantification

Indexed keywords

BIODIVERSITY; DATA REDUCTION; SEARCH ENGINES; TISSUE;

EID: 33847321126     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11103-006-9116-9     Document Type: Article
Times cited : (60)

References (43)
  • 1
    • 0034734040 scopus 로고    scopus 로고
    • Automated extraction of information in molecular biology
    • Andrade MA, Bork P (2000) Automated extraction of information in molecular biology. FEBS Lett 476:12-17
    • (2000) FEBS Lett , vol.476 , pp. 12-17
    • Andrade, M.A.1    Bork, P.2
  • 3
    • 0038589165 scopus 로고    scopus 로고
    • The anatomy of a large-scale hypertextual web search engine
    • Brin S, Page L (1998) The anatomy of a large-scale hypertextual web search engine. Comput Netw 30:107-117
    • (1998) Comput Netw , vol.30 , pp. 107-117
    • Brin, S.1    Page, L.2
  • 4
    • 12744274644 scopus 로고    scopus 로고
    • Identification of novel heat shock factor-dependent genes and biochemical pathways in Arabidopsis thaliana
    • Busch W, Wunderlich M, Schöffl F (2005) Identification of novel heat shock factor-dependent genes and biochemical pathways in Arabidopsis thaliana. Plant J 41:1-14
    • (2005) Plant J , vol.41 , pp. 1-14
    • Busch, W.1    Wunderlich, M.2    Schöffl, F.3
  • 5
    • 0036668567 scopus 로고    scopus 로고
    • Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): Trends and problems
    • Bustin SA (2002) Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. J Mol Endocrinol 29:23-39
    • (2002) J Mol Endocrinol , vol.29 , pp. 23-39
    • Bustin, S.A.1
  • 8
    • 0141995484 scopus 로고    scopus 로고
    • Selection of candidate housekeeping controls in tomato plants using EST data
    • Coker JS, Davis E (2003) Selection of candidate housekeeping controls in tomato plants using EST data. BioTechniques 35(4):740-748
    • (2003) BioTechniques , vol.35 , Issue.4 , pp. 740-748
    • Coker, J.S.1    Davis, E.2
  • 9
    • 32644481938 scopus 로고    scopus 로고
    • Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis
    • Czechowski T, Stitt M, Altmann T, Udvardi MK, Scheible W (2005) Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiol 139:5-17
    • (2005) Plant Physiol , vol.139 , pp. 5-17
    • Czechowski, T.1    Stitt, M.2    Altmann, T.3    Udvardi, M.K.4    Scheible, W.5
  • 10
  • 12
    • 0035696449 scopus 로고    scopus 로고
    • Expressed sequence tags from cold-acclimatized barley identify novel plant genes
    • Faccioli P, Pecchioni N, Cattivelli L, Stanca AM, Terzi V (2001) Expressed sequence tags from cold-acclimatized barley identify novel plant genes. Plant Breed 120:497-502
    • (2001) Plant Breed , vol.120 , pp. 497-502
    • Faccioli, P.1    Pecchioni, N.2    Cattivelli, L.3    Stanca, A.M.4    Terzi, V.5
  • 13
    • 18744375994 scopus 로고    scopus 로고
    • Analysis of differential expression of barley ESTs during cold acclimatization using microarray technology
    • Faccioli P, Lagonigro MS, De Cecco L, Stanca AM, Alberici R, Terzi V (2002) Analysis of differential expression of barley ESTs during cold acclimatization using microarray technology. Plant Biol 4:630-639
    • (2002) Plant Biol , vol.4 , pp. 630-639
    • Faccioli, P.1    Lagonigro, M.S.2    De Cecco, L.3    Stanca, A.M.4    Alberici, R.5    Terzi, V.6
  • 14
    • 24744468755 scopus 로고    scopus 로고
    • From single genes to co-expression networks: Extracting knowledge from barley functional genomics
    • Faccioli P, Provero P, Herrmann C, Stanca AM, Morcia C, Terzi V (2005) From single genes to co-expression networks: extracting knowledge from barley functional genomics. Plant Mol Biol 58(5):739-750
    • (2005) Plant Mol Biol , vol.58 , Issue.5 , pp. 739-750
    • Faccioli, P.1    Provero, P.2    Herrmann, C.3    Stanca, A.M.4    Morcia, C.5    Terzi, V.6
  • 15
    • 18944381809 scopus 로고    scopus 로고
    • Comparison of reference genes for quantitative real-time polymerase chain reaction analysis of gene expression in sugarcane
    • Iskandar HM, Simpson RS, Casu RE, Bonnett GD, MacLean DJ, Manners JM (2004) Comparison of reference genes for quantitative real-time polymerase chain reaction analysis of gene expression in sugarcane. Plant Mol Biol Rep 22:325-337
    • (2004) Plant Mol Biol Rep , vol.22 , pp. 325-337
    • Iskandar, H.M.1    Simpson, R.S.2    Casu, R.E.3    Bonnett, G.D.4    MacLean, D.J.5    Manners, J.M.6
  • 16
    • 0032534813 scopus 로고    scopus 로고
    • RNA quantitation by fluorescence-based solution assay: RiboGreen reagent characterization
    • Jones LJ, Yue ST, Cheung C, Singer VL (1998) RNA quantitation by fluorescence-based solution assay: RiboGreen reagent characterization. Anal Biochem 265:368-374
    • (1998) Anal Biochem , vol.265 , pp. 368-374
    • Jones, L.J.1    Yue, S.T.2    Cheung, C.3    Singer, V.L.4
  • 17
    • 0043192611 scopus 로고    scopus 로고
    • Selection of optimal internal controls for gene expression profiling of liver disease
    • Kim S, Kim T (2003) Selection of optimal internal controls for gene expression profiling of liver disease. BioTechniques 35:456-460
    • (2003) BioTechniques , vol.35 , pp. 456-460
    • Kim, S.1    Kim, T.2
  • 18
    • 0036178995 scopus 로고    scopus 로고
    • Control genes and variability: Absence of ubiquitous reference transcripts in diverse mammalian expression studies
    • Lee PD, Sladek R, Greenwood CMT, Hudson TJ (2002) Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies. Genome Res 12:292-297
    • (2002) Genome Res , vol.12 , pp. 292-297
    • Lee, P.D.1    Sladek, R.2    Greenwood, C.M.T.3    Hudson, T.J.4
  • 19
    • 0035710746 scopus 로고    scopus 로고
    • Analysis of relative gene expression data using real-time quantitative PCR and the 2-DDCt method
    • Livak KL, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-DDCt method. Methods 25:402-408
    • (2001) Methods , vol.25 , pp. 402-408
    • Livak, K.L.1    Schmittgen, T.D.2
  • 20
    • 1542374539 scopus 로고    scopus 로고
    • Two different heat shock transcription factors regulate immediate early expression of stress genes in Arabidopsis
    • Lohmann C, Eggers-Schumacher G, Wunderlich M, Schöffl F (2004) Two different heat shock transcription factors regulate immediate early expression of stress genes in Arabidopsis. Mol Genet Genomics 271:11-21
    • (2004) Mol Genet Genomics , vol.271 , pp. 11-21
    • Lohmann, C.1    Eggers-Schumacher, G.2    Wunderlich, M.3    Schöffl, F.4
  • 21
    • 0001186987 scopus 로고
    • Preliminary study of the inheritance of temperature stress proteins in barley (Hordeum vulgare L.)
    • Marmiroli N, Lorenzoni C, Stanca AM, Terzi V (1989) Preliminary study of the inheritance of temperature stress proteins in barley (Hordeum vulgare L.). Plant Sci 62:147-156
    • (1989) Plant Sci , vol.62 , pp. 147-156
    • Marmiroli, N.1    Lorenzoni, C.2    Stanca, A.M.3    Terzi, V.4
  • 22
    • 27144456802 scopus 로고    scopus 로고
    • Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress
    • Nicot N, Hausman J, Hoffmann L, Evers D (2005) Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress. J Exp Bot 56(421):2907-2914
    • (2005) J Exp Bot , vol.56 , Issue.421 , pp. 2907-2914
    • Nicot, N.1    Hausman, J.2    Hoffmann, L.3    Evers, D.4
  • 23
    • 33646002325 scopus 로고    scopus 로고
    • Identification and validation of suitable endogenous reference genes for gene expression studies of human bladder cancer
    • Ohl F, Jung M, Radonić A, Sachs M, Loening SA, Jung K (2006) Identification and validation of suitable endogenous reference genes for gene expression studies of human bladder cancer. J Urol 175:1915-1920
    • (2006) J Urol , vol.175 , pp. 1915-1920
    • Ohl, F.1    Jung, M.2    Radonić, A.3    Sachs, M.4    Loening, S.A.5    Jung, K.6
  • 25
    • 1842483281 scopus 로고    scopus 로고
    • Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper - excelbased tool using pair-wise correlations
    • Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP (2004) Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper - excelbased tool using pair-wise correlations. Biotechnol Lett 26:509-515
    • (2004) Biotechnol Lett , vol.26 , pp. 509-515
    • Pfaffl, M.W.1    Tichopad, A.2    Prgomet, C.3    Neuvians, T.P.4
  • 26
    • 0036898577 scopus 로고    scopus 로고
    • Microarray data normalization and transformation
    • Quackenbush J (2002) Microarray data normalization and transformation. Nat Genet 32(4s):496-501
    • (2002) Nat Genet , vol.32 , Issue.4 S , pp. 496-501
    • Quackenbush, J.1
  • 28
    • 1042272548 scopus 로고    scopus 로고
    • The housekeeping genes GAPDH and cyclophilin are regulated by metabolic state in the liver of dairy cows
    • Rhoads RP, McManaman C, Ingvartsen KL, Boisclair YR (2003) The housekeeping genes GAPDH and cyclophilin are regulated by metabolic state in the liver of dairy cows. J Dairy Sci 86:3423-3429
    • (2003) J Dairy Sci , vol.86 , pp. 3423-3429
    • Rhoads, R.P.1    McManaman, C.2    Ingvartsen, K.L.3    Boisclair, Y.R.4
  • 29
    • 24944531415 scopus 로고    scopus 로고
    • Semantic annotation of biomedical literature using Google
    • Gervasi O et al (eds) Computational science and its applications, ICCSA, Springer, Berlin Heidelberg New York, pp
    • Sætre R, Tveit A, Steigedal TS, Lægreid A (2005a) Semantic annotation of biomedical literature using Google. In: Gervasi O et al (eds) Computational science and its applications - ICCSA 2005, LNCS 3482. Springer, Berlin Heidelberg New York, pp 327-337
    • (2005) LNCS , vol.3482 , pp. 327-337
    • Sætre, R.1    Tveit, A.2    Steigedal, T.S.3    Lægreid, A.4
  • 30
    • 33745301179 scopus 로고    scopus 로고
    • gProt: Annotating protein interactions using Google and gene ontology. 9th International conference on knowledge-based & intelligent information & engineering systems
    • Springer, Berlin Heidelberg New York
    • Sætre R, Tveit A, Ranang MT, Steigedal TS, Thommensen L, Stunes K, Lægreid A (2005b) gProt: annotating protein interactions using Google and gene ontology. 9th International conference on knowledge-based & intelligent information & engineering systems (Lecture notes in artificial intelligence). Springer, Berlin Heidelberg New York
    • (2005) Lecture notes in artificial intelligence
    • Sætre, R.1    Tveit, A.2    Ranang, M.T.3    Steigedal, T.S.4    Thommensen, L.5    Stunes, K.6    Lægreid, A.7
  • 31
    • 0034694128 scopus 로고    scopus 로고
    • Effect of experimental treatment on housekeeping gene expression: Validation by real-time, quantitative RT-PCR
    • Schmittgen TD, Zakrajsek BA (2000) Effect of experimental treatment on housekeeping gene expression: validation by real-time, quantitative RT-PCR. J Biochem Biophys Methods 46:69-81
    • (2000) J Biochem Biophys Methods , vol.46 , pp. 69-81
    • Schmittgen, T.D.1    Zakrajsek, B.A.2
  • 33
    • 0032973950 scopus 로고    scopus 로고
    • New insights into an old protein: The functional diversity of mammalian glyceraldehyde-3-phosphate dehydrogenase
    • Sirover MA (1999) New insights into an old protein: the functional diversity of mammalian glyceraldehyde-3-phosphate dehydrogenase. Biochim Biophys Acta 1432:159-184
    • (1999) Biochim Biophys Acta , vol.1432 , pp. 159-184
    • Sirover, M.A.1
  • 34
    • 0034518635 scopus 로고    scopus 로고
    • The comparison of gene expression from multiple cDNA libraries
    • Stekel DJ, Git Y, Falciani F (2000) The comparison of gene expression from multiple cDNA libraries. Genome Res 10:2055-2061
    • (2000) Genome Res , vol.10 , pp. 2055-2061
    • Stekel, D.J.1    Git, Y.2    Falciani, F.3
  • 37
    • 33645558534 scopus 로고    scopus 로고
    • Comparative transcriptome analysis of barley and rice under salt stress
    • Ueda A, Kathiresan A, Bennett J, Takabe T (2006) Comparative transcriptome analysis of barley and rice under salt stress. Theor Appl Genet 112:1286-1294
    • (2006) Theor Appl Genet , vol.112 , pp. 1286-1294
    • Ueda, A.1    Kathiresan, A.2    Bennett, J.3    Takabe, T.4
  • 38
    • 0037129827 scopus 로고    scopus 로고
    • Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3(7):research0034.1-0034.11
    • Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3(7):research0034.1-0034.11
  • 39
    • 0141941592 scopus 로고    scopus 로고
    • Heat-stress-dependency and developmental modulation of gene expression: The potential of house-keeping genes as internal standards in mRNA expression profiling using real-time RT-PCR
    • Volkov RA, Panchuk II, Schoffl F (2003) Heat-stress-dependency and developmental modulation of gene expression: the potential of house-keeping genes as internal standards in mRNA expression profiling using real-time RT-PCR. J Exp Bot 54:2343-2349
    • (2003) J Exp Bot , vol.54 , pp. 2343-2349
    • Volkov, R.A.1
  • 41
    • 0034720002 scopus 로고    scopus 로고
    • Comparison of human adult and fetal expression and identification of 535 housekeeping/ maintenance genes
    • Warrington J, Nair A, Mahadevappa M, Tsyganskaya M (2000) Comparison of human adult and fetal expression and identification of 535 housekeeping/ maintenance genes. Physiol Genomics 2:143-147
    • (2000) Physiol Genomics , vol.2 , pp. 143-147
    • Warrington, J.1    Nair, A.2    Mahadevappa, M.3    Tsyganskaya, M.4
  • 42
    • 0027244853 scopus 로고
    • The p53-mdm-2 autoregulatory feedback loop
    • Wu X, Bayle JH, Olson D, Levine AJ (1993) The p53-mdm-2 autoregulatory feedback loop. Genes Dev 7:1126-1132
    • (1993) Genes Dev , vol.7 , pp. 1126-1132
    • Wu, X.1    Bayle, J.H.2    Olson, D.3    Levine, A.J.4
  • 43
    • 33646365324 scopus 로고    scopus 로고
    • Selection of internal control genes for real-time quantitative RT-PCR assays in the oomycete plant pathogen Phytophthora parasitica
    • Yan HZ, Liou RF (2006) Selection of internal control genes for real-time quantitative RT-PCR assays in the oomycete plant pathogen Phytophthora parasitica. Fungal Genet Biol 43:430-438
    • (2006) Fungal Genet Biol , vol.43 , pp. 430-438
    • Yan, H.Z.1    Liou, R.F.2


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