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Volumn 8, Issue 1, 2015, Pages

ITAP: Integrated transcriptomics and phenotype database for stress response of Escherichia coli and Saccharomyces cerevisiae Bioinformatics

Author keywords

Escherichia coli; Open source; Transcriptomics phenotype correlation; Yeast

Indexed keywords

TRANSCRIPTOME;

EID: 84958931762     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/s13104-015-1759-7     Document Type: Article
Times cited : (2)

References (29)
  • 1
    • 0004268763 scopus 로고    scopus 로고
    • American Society for Microbiology Press Washington, DC
    • Storz G, Hengge R. Bacterial stress responses. Washington, DC: American Society for Microbiology Press; 2010.
    • (2010) Bacterial Stress Responses
    • Storz, G.1    Hengge, R.2
  • 2
    • 0034987011 scopus 로고    scopus 로고
    • General stress response of Bacillus subtilis and other bacteria
    • New York: Academic Press
    • Hecker M, Völker U. General stress response of Bacillus subtilis and other bacteria. In: Advances in microbial physiology. vol 44. New York: Academic Press; 2001. p. 35-91.
    • (2001) Advances in Microbial Physiology , vol.44 , pp. 35-91
    • Hecker, M.1    Völker, U.2
  • 3
    • 14944350031 scopus 로고    scopus 로고
    • Adaptation of microorganisms to cold temperatures, weak acid preservatives, low pH, and osmotic stress: A review
    • 1:CAS:528:DC%2BD2cXjvFGiur4%3D
    • Beales N. Adaptation of microorganisms to cold temperatures, weak acid preservatives, low pH, and osmotic stress: A review. Compr Rev Food Sci Food Saf. 2004;3(1):1-20.
    • (2004) Compr Rev Food Sci Food Saf , vol.3 , Issue.1 , pp. 1-20
    • Beales, N.1
  • 5
    • 78650598564 scopus 로고    scopus 로고
    • Adaptive response to oxidative stress: Bacteria, fungi, plants and animals
    • Lushchak VI. Adaptive response to oxidative stress: bacteria, fungi, plants and animals. Comp Biochem Physiol C: Toxicol Pharmacol. 2011;153(2):175-90.
    • (2011) Comp Biochem Physiol C: Toxicol Pharmacol , vol.153 , Issue.2 , pp. 175-190
    • Lushchak, V.I.1
  • 6
    • 78549260740 scopus 로고    scopus 로고
    • Comparative transcriptome profiling analyses during the lag phase uncover YAP1, PDR1, PDR3, RPN4, and HSF1 as key regulatory genes in genomic adaptation to the lignocellulose derived inhibitor HMF for Saccharomyces cerevisiae
    • 1:CAS:528:DC%2BC3cXhsFagt73K
    • Ma M, Liu ZL. Comparative transcriptome profiling analyses during the lag phase uncover YAP1, PDR1, PDR3, RPN4, and HSF1 as key regulatory genes in genomic adaptation to the lignocellulose derived inhibitor HMF for Saccharomyces cerevisiae. BMC Genom. 2010;11:660.
    • (2010) BMC Genom , vol.11 , pp. 660
    • Ma, M.1    Liu, Z.L.2
  • 7
    • 34547868108 scopus 로고    scopus 로고
    • Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae
    • 1:CAS:528:DC%2BD2sXhtVWntbjK 17484738
    • Abbott DA, Knijnenburg TA, de Poorter LMI, Reinders MJT, Pronk JT, van Maris AJA. Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res. 2007;7:819-33.
    • (2007) FEMS Yeast Res , vol.7 , pp. 819-833
    • Abbott, D.A.1    Knijnenburg, T.A.2    De Poorter, L.M.I.3    Reinders, M.J.T.4    Pronk, J.T.5    Van Maris, A.J.A.6
  • 8
    • 84925067568 scopus 로고    scopus 로고
    • Tolerance to acetic acid is improved by mutations of the TATA-binding protein gene
    • 1:CAS:528:DC%2BC2MXkvVKhsro%3D 24761971
    • An J, Kwon H, Kim E, Lee YM, Ko HJ, Park H, Choi I-G, Kim S, Kim KH, Kim W, et al. Tolerance to acetic acid is improved by mutations of the TATA-binding protein gene. Environ Microbiol. 2015;17(3):656-69.
    • (2015) Environ Microbiol , vol.17 , Issue.3 , pp. 656-669
    • An, J.1    Kwon, H.2    Kim, E.3    Lee, Y.M.4    Ko, H.J.5    Park, H.6    Choi, I.-G.7    Kim, S.8    Kim, K.H.9    Kim, W.10
  • 9
    • 59849096620 scopus 로고    scopus 로고
    • Comparative lipidomics of four strains of Saccharomyces cerevisiae reveals different responses to furfural, phenol, and acetic acid
    • 1:CAS:528:DC%2BD1cXhsVCrurbK 19049411
    • Xia J-M, Yuan Y-J. Comparative lipidomics of four strains of Saccharomyces cerevisiae reveals different responses to furfural, phenol, and acetic acid. J Agric Food Chem. 2009;57(1):99-108.
    • (2009) J Agric Food Chem , vol.57 , Issue.1 , pp. 99-108
    • Xia, J.-M.1    Yuan, Y.-J.2
  • 10
    • 12844281816 scopus 로고    scopus 로고
    • Two-dimensional transcriptome analysis in chemostat cultures: Combinatorial effects of oxygen availability and macronutrient limitation in Saccharomyces cerevisiae
    • 1:CAS:528:DC%2BD2cXhtFGgu7nM 15496405
    • Tai SL, Boer VM, Daran-Lapujade P, Walsh MC, de Winde JH, Daran J-M, Pronk JT. Two-dimensional transcriptome analysis in chemostat cultures: combinatorial effects of oxygen availability and macronutrient limitation in Saccharomyces cerevisiae. J Biol Chem. 2005;280(1):437-47.
    • (2005) J Biol Chem , vol.280 , Issue.1 , pp. 437-447
    • Tai, S.L.1    Boer, V.M.2    Daran-Lapujade, P.3    Walsh, M.C.4    De Winde, J.H.5    Daran, J.-M.6    Pronk, J.T.7
  • 13
    • 34250338693 scopus 로고    scopus 로고
    • Microbial stress-response physiology and its implications for ecosystem function
    • 17601131
    • Schimel J, Balser TC, Wallenstein M. Microbial stress-response physiology and its implications for ecosystem function. Ecology. 2007;88(6):1386-94.
    • (2007) Ecology , vol.88 , Issue.6 , pp. 1386-1394
    • Schimel, J.1    Balser, T.C.2    Wallenstein, M.3
  • 14
    • 15044340553 scopus 로고    scopus 로고
    • Evolutionary engineering of multiple-stress resistant Saccharomyces cerevisiae
    • 15780656
    • Çakar ZP, Seker UOS, Tamerler C, Sonderegger M, Sauer U. Evolutionary engineering of multiple-stress resistant Saccharomyces cerevisiae. FEMS Yeast Res. 2005;5(6-7):569-78.
    • (2005) FEMS Yeast Res , vol.5 , Issue.6-7 , pp. 569-578
    • Çakar, Z.P.1    Seker, U.O.S.2    Tamerler, C.3    Sonderegger, M.4    Sauer, U.5
  • 15
    • 15544377794 scopus 로고    scopus 로고
    • Molecular and evolutionary basis of the cellular stress response
    • 15709958
    • Kültz D. Molecular and evolutionary basis of the cellular stress response. Annu Rev Physiol. 2005;67(1):225-57.
    • (2005) Annu Rev Physiol , vol.67 , Issue.1 , pp. 225-257
    • Kültz, D.1
  • 16
    • 0032810422 scopus 로고    scopus 로고
    • Microbial stress response in minimal processing
    • 1:CAS:528:DyaK1MXmsVarsL4%3D 10488845
    • Abee T, Wouters JA. Microbial stress response in minimal processing. Int J Food Microbiol. 1999;50(1-2):65-91.
    • (1999) Int J Food Microbiol , vol.50 , Issue.1-2 , pp. 65-91
    • Abee, T.1    Wouters, J.A.2
  • 18
    • 0036024730 scopus 로고    scopus 로고
    • Evaluating the role of microbial stress response mechanisms in causing biological treatment system upset
    • 1:CAS:528:DC%2BD3sXhsFajuw%3D%3D 12216609
    • Love N, Bott C. Evaluating the role of microbial stress response mechanisms in causing biological treatment system upset. Water Sci Technol. 2002;46(1-2):11-8.
    • (2002) Water Sci Technol , vol.46 , Issue.1-2 , pp. 11-18
    • Love, N.1    Bott, C.2
  • 19
    • 73249132552 scopus 로고    scopus 로고
    • Resistance of Saccharomyces cerevisiae to high concentrations of furfural is based on NADPH-dependent reduction by at least two oxireductases
    • 2794096 1:CAS:528:DC%2BD1MXhs1Whu7fE 19854918
    • Heer D, Heine D, Sauer U. Resistance of Saccharomyces cerevisiae to high concentrations of furfural is based on NADPH-dependent reduction by at least two oxireductases. Appl Environ Microbiol. 2009;75(24):7631-8.
    • (2009) Appl Environ Microbiol , vol.75 , Issue.24 , pp. 7631-7638
    • Heer, D.1    Heine, D.2    Sauer, U.3
  • 20
    • 33845699793 scopus 로고    scopus 로고
    • NCBI GEO standards and services for microarray data
    • 2270403 1:CAS:528:DC%2BD28Xht12gtb%2FK 17160034
    • Edgar R, Barrett T. NCBI GEO standards and services for microarray data. Nat Biotechnol. 2006;24(12):1471-2.
    • (2006) Nat Biotechnol , vol.24 , Issue.12 , pp. 1471-1472
    • Edgar, R.1    Barrett, T.2
  • 23
    • 0032893434 scopus 로고    scopus 로고
    • The EMBL nucleotide sequence database
    • 148088 1:CAS:528:DyaK1MXpsVGlsQ%3D%3D 9847133
    • Stoesser G, Tuli MA, Lopez R, Sterk P. The EMBL nucleotide sequence database. Nucleic Acids Res. 1999;27(1):18-24.
    • (1999) Nucleic Acids Res , vol.27 , Issue.1 , pp. 18-24
    • Stoesser, G.1    Tuli, M.A.2    Lopez, R.3    Sterk, P.4
  • 25
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • 1:CAS:528:DyaK2MXovVersLk%3D 7569999
    • Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995;270(5235):467-70.
    • (1995) Science , vol.270 , Issue.5235 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 26
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • 2949280 1:CAS:528:DC%2BD1cXhsFWis7bL 19015660
    • Wang Z, Gerstein M, Snyder M. RNA-Seq: A revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10(1):57-63.
    • (2009) Nat Rev Genet , vol.10 , Issue.1 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 28
    • 84958944106 scopus 로고    scopus 로고
    • Plot Digitizer: GPL. Available Accessed 2013 May 6
    • Huwaldt JA. Plot Digitizer: GPL. Available: http://plotdigitizer.sourceforge.net/. Accessed 2013 May 6.
    • Huwaldt, J.A.1
  • 29
    • 84972537246 scopus 로고
    • Francis Galton's account of the invention of correlation
    • Stigler SM. Francis Galton's account of the invention of correlation. Stat Sci. 1989;4(2):73-9.
    • (1989) Stat Sci , vol.4 , Issue.2 , pp. 73-79
    • Stigler, S.M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.