메뉴 건너뛰기




Volumn 15, Issue 1, 2014, Pages

AlgaePath: Comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae

Author keywords

Algae; Gene expression; Next generation sequencing; Pathway; Systems biology

Indexed keywords

NITROGEN; SULFUR;

EID: 84899063455     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-196     Document Type: Article
Times cited : (35)

References (36)
  • 1
    • 0036163611 scopus 로고    scopus 로고
    • Energy production from biomass (part 1): overview of biomass
    • 10.1016/S0960-8524(01)00118-3, 12058829
    • McKendry P. Energy production from biomass (part 1): overview of biomass. Bioresour Technol 2002, 83(1):37-46. 10.1016/S0960-8524(01)00118-3, 12058829.
    • (2002) Bioresour Technol , vol.83 , Issue.1 , pp. 37-46
    • McKendry, P.1
  • 2
    • 0036161536 scopus 로고    scopus 로고
    • Energy production from biomass (part 2): conversion technologies
    • 10.1016/S0960-8524(01)00119-5, 12058830
    • McKendry P. Energy production from biomass (part 2): conversion technologies. Bioresour Technol 2002, 83(1):47-54. 10.1016/S0960-8524(01)00119-5, 12058830.
    • (2002) Bioresour Technol , vol.83 , Issue.1 , pp. 47-54
    • McKendry, P.1
  • 3
    • 78649512519 scopus 로고    scopus 로고
    • First generation biofuels compete
    • 10.1016/j.nbt.2010.06.010, 20601265
    • Martin MA. First generation biofuels compete. N Biotechnol 2010, 27(5):596-608. 10.1016/j.nbt.2010.06.010, 20601265.
    • (2010) N Biotechnol , vol.27 , Issue.5 , pp. 596-608
    • Martin, M.A.1
  • 4
    • 84865203808 scopus 로고    scopus 로고
    • Oil accumulation is controlled by carbon precursor supply for fatty acid synthesis in Chlamydomonas reinhardtii
    • 10.1093/pcp/pcs082, 22642988
    • Fan J, Yan C, Andre C, Shanklin J, Schwender J, Xu C. Oil accumulation is controlled by carbon precursor supply for fatty acid synthesis in Chlamydomonas reinhardtii. Plant Cell Physiol 2012, 53(8):1380-1390. 10.1093/pcp/pcs082, 22642988.
    • (2012) Plant Cell Physiol , vol.53 , Issue.8 , pp. 1380-1390
    • Fan, J.1    Yan, C.2    Andre, C.3    Shanklin, J.4    Schwender, J.5    Xu, C.6
  • 5
    • 77957042696 scopus 로고    scopus 로고
    • Commercialization potential of microalgae for biofuels production
    • Singh J, Gu S. Commercialization potential of microalgae for biofuels production. Renew Sust Energ Rev 2010, 14(9):2596-2610.
    • (2010) Renew Sust Energ Rev , vol.14 , Issue.9 , pp. 2596-2610
    • Singh, J.1    Gu, S.2
  • 7
    • 0005468265 scopus 로고    scopus 로고
    • A comparative study on heavy metal biosorption characteristics of some algae
    • Çetinkaya Dönmez G, Aksu Z, Öztürk A, Kutsal T. A comparative study on heavy metal biosorption characteristics of some algae. Process Biochem 1999, 34(9):885-892.
    • (1999) Process Biochem , vol.34 , Issue.9 , pp. 885-892
    • Çetinkaya Dönmez, G.1    Aksu, Z.2    Öztürk, A.3    Kutsal, T.4
  • 8
    • 0027395832 scopus 로고
    • Adsorption of heavy metals by green algae and ground rice hulls
    • Roy D, Greenlaw PN, Shane BS. Adsorption of heavy metals by green algae and ground rice hulls. J Environ Sci Health Part A 1993, 28(1):37-50.
    • (1993) J Environ Sci Health Part A , vol.28 , Issue.1 , pp. 37-50
    • Roy, D.1    Greenlaw, P.N.2    Shane, B.S.3
  • 9
    • 0034815945 scopus 로고    scopus 로고
    • Biosorption of Chromium (VI) from Aqueous solutions by green algae spirogyra species
    • 10.1016/S0043-1354(01)00138-5, 11791837
    • Gupta V, Shrivastava A, Jain N. Biosorption of Chromium (VI) from Aqueous solutions by green algae spirogyra species. Water Res 2001, 35(17):4079-4085. 10.1016/S0043-1354(01)00138-5, 11791837.
    • (2001) Water Res , vol.35 , Issue.17 , pp. 4079-4085
    • Gupta, V.1    Shrivastava, A.2    Jain, N.3
  • 11
    • 0026379430 scopus 로고
    • Role of the marine biosphere in the global carbon cycle
    • Longhurst AR. Role of the marine biosphere in the global carbon cycle. Limnol Oceanogr 1991, 36(8):1507-1526.
    • (1991) Limnol Oceanogr , vol.36 , Issue.8 , pp. 1507-1526
    • Longhurst, A.R.1
  • 12
    • 80052057468 scopus 로고    scopus 로고
    • Characterization of a green microalga UTEX 2219-4: effects of photosynthesis and osmotic stress on oil body formation
    • Wang ST, Pan YY, Liu CC, Chuang LT, Chen CNN. Characterization of a green microalga UTEX 2219-4: effects of photosynthesis and osmotic stress on oil body formation. Bot Stud 2011, 52(3):305-312.
    • (2011) Bot Stud , vol.52 , Issue.3 , pp. 305-312
    • Wang, S.T.1    Pan, Y.Y.2    Liu, C.C.3    Chuang, L.T.4    Chen, C.N.N.5
  • 14
    • 84863104468 scopus 로고    scopus 로고
    • Transcriptome-wide changes in Chlamydomonas reinhardtii gene expression regulated by carbon dioxide and the CO2-concentrating mechanism regulator CIA5/CCM1
    • 10.1105/tpc.112.097949, 3442575, 22634760
    • Fang W, Si Y, Douglass S, Casero D, Merchant SS, Pellegrini M, Ladunga I, Liu P, Spalding MH. Transcriptome-wide changes in Chlamydomonas reinhardtii gene expression regulated by carbon dioxide and the CO2-concentrating mechanism regulator CIA5/CCM1. Plant Cell 2012, 24(5):1876-1893. 10.1105/tpc.112.097949, 3442575, 22634760.
    • (2012) Plant Cell , vol.24 , Issue.5 , pp. 1876-1893
    • Fang, W.1    Si, Y.2    Douglass, S.3    Casero, D.4    Merchant, S.S.5    Pellegrini, M.6    Ladunga, I.7    Liu, P.8    Spalding, M.H.9
  • 16
    • 77955686486 scopus 로고    scopus 로고
    • RNA-seq analysis of sulfur-deprived Chlamydomonas cells reveals aspects of acclimation critical for cell survival
    • 10.1105/tpc.109.071167, 2910963, 20587772
    • Gonzalez-Ballester D, Casero D, Cokus S, Pellegrini M, Merchant SS, Grossman AR. RNA-seq analysis of sulfur-deprived Chlamydomonas cells reveals aspects of acclimation critical for cell survival. Plant Cell 2010, 22(6):2058-2084. 10.1105/tpc.109.071167, 2910963, 20587772.
    • (2010) Plant Cell , vol.22 , Issue.6 , pp. 2058-2084
    • Gonzalez-Ballester, D.1    Casero, D.2    Cokus, S.3    Pellegrini, M.4    Merchant, S.S.5    Grossman, A.R.6
  • 18
    • 84859991534 scopus 로고    scopus 로고
    • Impact of oxidative stress on ascorbate biosynthesis in Chlamydomonas via regulation of the VTC2 gene encoding a GDP-L-galactose phosphorylase
    • 10.1074/jbc.M112.341982, 3340187, 22393048
    • Urzica EI, Adler LN, Page MD, Linster CL, Arbing MA, Casero D, Pellegrini M, Merchant SS, Clarke SG. Impact of oxidative stress on ascorbate biosynthesis in Chlamydomonas via regulation of the VTC2 gene encoding a GDP-L-galactose phosphorylase. J Biol Chem 2012, 287(17):14234-14245. 10.1074/jbc.M112.341982, 3340187, 22393048.
    • (2012) J Biol Chem , vol.287 , Issue.17 , pp. 14234-14245
    • Urzica, E.I.1    Adler, L.N.2    Page, M.D.3    Linster, C.L.4    Arbing, M.A.5    Casero, D.6    Pellegrini, M.7    Merchant, S.S.8    Clarke, S.G.9
  • 20
    • 84866080959 scopus 로고    scopus 로고
    • BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species
    • Patel RV, Nahal HK, Breit R, Provart NJ. BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species. Plant J cCell Mole Biol 2012, 71(6):1038-1050.
    • (2012) Plant J cCell Mole Biol , vol.71 , Issue.6 , pp. 1038-1050
    • Patel, R.V.1    Nahal, H.K.2    Breit, R.3    Provart, N.J.4
  • 21
    • 84855882668 scopus 로고    scopus 로고
    • Browsing metabolic and regulatory networks with BioCyc
    • 10.1007/978-1-61779-361-5_11, 3549617, 22144155
    • Latendresse M, Paley S, Karp PD. Browsing metabolic and regulatory networks with BioCyc. Methods Mol Biol 2012, 804:197-216. 10.1007/978-1-61779-361-5_11, 3549617, 22144155.
    • (2012) Methods Mol Biol , vol.804 , pp. 197-216
    • Latendresse, M.1    Paley, S.2    Karp, P.D.3
  • 22
    • 79960158139 scopus 로고    scopus 로고
    • Algal functional annotation tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data
    • Lopez D, Casero D, Cokus SJ, Merchant SS, Pellegrini M. Algal functional annotation tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data. BMC Bioinform 2011, 12:282.
    • (2011) BMC Bioinform , vol.12 , pp. 282
    • Lopez, D.1    Casero, D.2    Cokus, S.J.3    Merchant, S.S.4    Pellegrini, M.5
  • 25
    • 84874969184 scopus 로고    scopus 로고
    • PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees
    • 3531194, 23193289
    • Mi H, Muruganujan A, Thomas PD. PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res 2013, 41(Database issue):D377-D386. 3531194, 23193289.
    • (2013) Nucleic Acids Res , vol.41 , Issue.Database issue Database issue
    • Mi, H.1    Muruganujan, A.2    Thomas, P.D.3
  • 27
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • 10.1038/nmeth.1923, 3322381, 22388286
    • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9(4):357-359. 10.1038/nmeth.1923, 3322381, 22388286.
    • (2012) Nat Methods , vol.9 , Issue.4 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 28
    • 0036226603 scopus 로고    scopus 로고
    • BLAT---the BLAST-like alignment tool
    • 10.1101/gr.229202. Article published online before March 2002, 187518, 11932250
    • Kent WJ. BLAT---the BLAST-like alignment tool. Genome Res 2002, 12(4):656-664. 10.1101/gr.229202. Article published online before March 2002, 187518, 11932250.
    • (2002) Genome Res , vol.12 , Issue.4 , pp. 656-664
    • Kent, W.J.1
  • 30
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: kyoto encyclopedia of genes and genomes
    • 10.1093/nar/28.1.27, 102409, 10592173
    • Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28(1):27-30. 10.1093/nar/28.1.27, 102409, 10592173.
    • (2000) Nucleic Acids Res , vol.28 , Issue.1 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 32
    • 53049102292 scopus 로고    scopus 로고
    • A green light for engineered algae: redirecting metabolism to fuel a biotechnology revolution
    • Rosenberg JN, Oyler GA, Wilkinson L, Betenbaugh MJ. A green light for engineered algae: redirecting metabolism to fuel a biotechnology revolution. Curr Opin Biol 2008, 19(5):430-436.
    • (2008) Curr Opin Biol , vol.19 , Issue.5 , pp. 430-436
    • Rosenberg, J.N.1    Oyler, G.A.2    Wilkinson, L.3    Betenbaugh, M.J.4
  • 33
    • 79952501970 scopus 로고    scopus 로고
    • Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: pathway description and gene discovery for production of next-generation biofuels
    • 10.1186/1471-2164-12-148, 3061936, 21401935
    • Rismani-Yazdi H, Haznedaroglu BZ, Bibby K, Peccia J. Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: pathway description and gene discovery for production of next-generation biofuels. BMC Genomics 2011, 12:148. 10.1186/1471-2164-12-148, 3061936, 21401935.
    • (2011) BMC Genomics , vol.12 , pp. 148
    • Rismani-Yazdi, H.1    Haznedaroglu, B.Z.2    Bibby, K.3    Peccia, J.4
  • 34
    • 73349097525 scopus 로고    scopus 로고
    • Algal lipid bodies: stress induction, purification, and biochemical characterization in wild-type and starchless Chlamydomonas reinhardtii
    • 10.1128/EC.00272-09, 2794211, 19880756
    • Wang ZT, Ullrich N, Joo S, Waffenschmidt S, Goodenough U. Algal lipid bodies: stress induction, purification, and biochemical characterization in wild-type and starchless Chlamydomonas reinhardtii. Eukaryot Cell 2009, 8(12):1856-1868. 10.1128/EC.00272-09, 2794211, 19880756.
    • (2009) Eukaryot Cell , vol.8 , Issue.12 , pp. 1856-1868
    • Wang, Z.T.1    Ullrich, N.2    Joo, S.3    Waffenschmidt, S.4    Goodenough, U.5
  • 35
    • 6344221872 scopus 로고    scopus 로고
    • Insights into the survival of Chlamydomonas reinhardtii during sulfur starvation based on microarray analysis of gene expression
    • 10.1128/EC.3.5.1331-1348.2004, 522608, 15470261
    • Zhang Z, Shrager J, Jain M, Chang CW, Vallon O, Grossman AR. Insights into the survival of Chlamydomonas reinhardtii during sulfur starvation based on microarray analysis of gene expression. Eukaryot Cell 2004, 3(5):1331-1348. 10.1128/EC.3.5.1331-1348.2004, 522608, 15470261.
    • (2004) Eukaryot Cell , vol.3 , Issue.5 , pp. 1331-1348
    • Zhang, Z.1    Shrager, J.2    Jain, M.3    Chang, C.W.4    Vallon, O.5    Grossman, A.R.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.