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Volumn 8, Issue 4, 2013, Pages

Network Theory Inspired Analysis of Time-Resolved Expression Data Reveals Key Players Guiding P. patens Stem Cell Development

Author keywords

[No Author keywords available]

Indexed keywords

BASIC HELIX LOOP HELIX TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR; TRANSCRIPTOME;

EID: 84876337994     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0060494     Document Type: Article
Times cited : (12)

References (40)
  • 1
    • 84888870145 scopus 로고    scopus 로고
    • Local Cues and Asymmetric Cell Divisions Underpin Body Plan Transitions in the Moss Physcomitrella patens
    • Harrison CJ, Roeder AH, Meyerowitz EM, Langdale JA, (2009) Local Cues and Asymmetric Cell Divisions Underpin Body Plan Transitions in the Moss Physcomitrella patens. Curr Biol 18: 18.
    • (2009) Curr Biol , vol.18 , pp. 18
    • Harrison, C.J.1    Roeder, A.H.2    Meyerowitz, E.M.3    Langdale, J.A.4
  • 2
    • 69449106863 scopus 로고    scopus 로고
    • Regulation of stem cell maintenance by the Polycomb protein FIE has been conserved during land plant evolution
    • Mosquna A, Katz A, Decker EL, Rensing SA, Reski R, et al. (2009) Regulation of stem cell maintenance by the Polycomb protein FIE has been conserved during land plant evolution. Development 136: 2433-2444.
    • (2009) Development , vol.136 , pp. 2433-2444
    • Mosquna, A.1    Katz, A.2    Decker, E.L.3    Rensing, S.A.4    Reski, R.5
  • 3
    • 80053213807 scopus 로고    scopus 로고
    • Physcomitrella Cyclin-Dependent Kinase A Links Cell Cycle Reactivation to Other Cellular Changes during Reprogramming of Leaf Cells
    • Ishikawa M, Murata T, Sato Y, Nishiyama T, Hiwatashi Y, et al. (2011) Physcomitrella Cyclin-Dependent Kinase A Links Cell Cycle Reactivation to Other Cellular Changes during Reprogramming of Leaf Cells. Plant Cell 23: 2924-2938.
    • (2011) Plant Cell , vol.23 , pp. 2924-2938
    • Ishikawa, M.1    Murata, T.2    Sato, Y.3    Nishiyama, T.4    Hiwatashi, Y.5
  • 5
    • 77957762129 scopus 로고    scopus 로고
    • Dynamic interaction networks in a hierarchically organized tissue
    • Kirouac DC, Ito C, Csaszar E, Roch A, Yu M, et al. (2010) Dynamic interaction networks in a hierarchically organized tissue. Mol Syst Biol 6: 417.
    • (2010) Mol Syst Biol , vol.6 , pp. 417
    • Kirouac, D.C.1    Ito, C.2    Csaszar, E.3    Roch, A.4    Yu, M.5
  • 6
    • 77949403895 scopus 로고    scopus 로고
    • Zebrafish Pou5f1-dependent transcriptional networks in temporal control of early development
    • Onichtchouk D, Geier F, Polok B, Messerschmidt DM, Mossner R, et al. (2010) Zebrafish Pou5f1-dependent transcriptional networks in temporal control of early development. Mol Syst Biol 6: 354.
    • (2010) Mol Syst Biol , vol.6 , pp. 354
    • Onichtchouk, D.1    Geier, F.2    Polok, B.3    Messerschmidt, D.M.4    Mossner, R.5
  • 8
    • 34247217200 scopus 로고    scopus 로고
    • Hubs in biological interaction networks exhibit low changes in expression in experimental asthma
    • Lu X, Jain VV, Finn PW, Perkins DL, (2007) Hubs in biological interaction networks exhibit low changes in expression in experimental asthma. Mol Syst Biol 3: 98.
    • (2007) Mol Syst Biol , vol.3 , pp. 98
    • Lu, X.1    Jain, V.V.2    Finn, P.W.3    Perkins, D.L.4
  • 9
    • 80052308980 scopus 로고    scopus 로고
    • Variance of gene expression identifies altered network constraints in neurological disease
    • Mar JC, Matigian NA, Mackay-Sim A, Mellick GD, Sue CM, et al. (2011) Variance of gene expression identifies altered network constraints in neurological disease. PLoS Genet 7: e1002207.
    • (2011) PLoS Genet , vol.7
    • Mar, J.C.1    Matigian, N.A.2    Mackay-Sim, A.3    Mellick, G.D.4    Sue, C.M.5
  • 10
    • 84861966141 scopus 로고    scopus 로고
    • Cancer core modules identification through genomic and transcriptomic changes correlation detection at network level
    • Li W, Wang R, Bai L, Yan Z, Sun Z, (2012) Cancer core modules identification through genomic and transcriptomic changes correlation detection at network level. BMC Syst Biol 6: 64.
    • (2012) BMC Syst Biol , vol.6 , pp. 64
    • Li, W.1    Wang, R.2    Bai, L.3    Yan, Z.4    Sun, Z.5
  • 11
    • 0014489272 scopus 로고
    • Metabolic stability and epigenesis in randomly constructed genetic nets
    • Kauffman SA, (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol 22: 437-467.
    • (1969) J Theor Biol , vol.22 , pp. 437-467
    • Kauffman, S.A.1
  • 12
    • 63749102693 scopus 로고    scopus 로고
    • Emergent genome-wide control in wildtype and genetically mutated lipopolysaccarides-stimulated macrophages
    • Tsuchiya M, Piras V, Choi S, Akira S, Tomita M, et al. (2009) Emergent genome-wide control in wildtype and genetically mutated lipopolysaccarides-stimulated macrophages. PLoS ONE 4: e4905.
    • (2009) PLoS ONE , vol.4
    • Tsuchiya, M.1    Piras, V.2    Choi, S.3    Akira, S.4    Tomita, M.5
  • 13
    • 77954256270 scopus 로고    scopus 로고
    • The molecular and physiological response of Physcomitrella patens to UV-B radiation
    • Wolf L, Rizzini L, Stracke R, Ulm R, Rensing SA, (2010) The molecular and physiological response of Physcomitrella patens to UV-B radiation. Plant Physiol 153: 1123-1134.
    • (2010) Plant Physiol , vol.153 , pp. 1123-1134
    • Wolf, L.1    Rizzini, L.2    Stracke, R.3    Ulm, R.4    Rensing, S.A.5
  • 14
    • 84888884631 scopus 로고    scopus 로고
    • Heterologous Expression and Functional Characterization of a Physcomitrella Pseudo Response Regulator Homolog, PpPRR2, in Arabidopsis
    • Satbhai SB, Yamashino T, Mizuno T, Aoki S, (2011) Heterologous Expression and Functional Characterization of a Physcomitrella Pseudo Response Regulator Homolog, PpPRR2, in Arabidopsis. Biosci Biotechnol Biochem 2011: 22.
    • (2011) Biosci Biotechnol Biochem , vol.2011 , pp. 22
    • Satbhai, S.B.1    Yamashino, T.2    Mizuno, T.3    Aoki, S.4
  • 15
    • 0035108613 scopus 로고    scopus 로고
    • Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis
    • Schaffer R, Landgraf J, Accerbi M, Simon V, Larson M, et al. (2001) Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis. Plant Cell 13: 113-123.
    • (2001) Plant Cell , vol.13 , pp. 113-123
    • Schaffer, R.1    Landgraf, J.2    Accerbi, M.3    Simon, V.4    Larson, M.5
  • 16
    • 77953380723 scopus 로고    scopus 로고
    • Does the core circadian clock in the moss Physcomitrella patens (Bryophyta) comprise a single loop?
    • Holm K, Kallman T, Gyllenstrand N, Hedman H, Lagercrantz U, (2010) Does the core circadian clock in the moss Physcomitrella patens (Bryophyta) comprise a single loop? BMC Plant Biol 10: 109.
    • (2010) BMC Plant Biol , vol.10 , pp. 109
    • Holm, K.1    Kallman, T.2    Gyllenstrand, N.3    Hedman, H.4    Lagercrantz, U.5
  • 17
    • 84888880650 scopus 로고    scopus 로고
    • Functional characterization of CCA1/LHY homolog genes, PpCCA1a and PpCCA1b, in the moss Physcomitrella patens
    • Okada R, Kondo S, Satbhai SB, Yamaguchi N, Tsukuda M, et al. (2009) Functional characterization of CCA1/LHY homolog genes, PpCCA1a and PpCCA1b, in the moss Physcomitrella patens. Plant J 16: 16.
    • (2009) Plant J , vol.16 , pp. 16
    • Okada, R.1    Kondo, S.2    Satbhai, S.B.3    Yamaguchi, N.4    Tsukuda, M.5
  • 18
    • 32144464541 scopus 로고    scopus 로고
    • Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms
    • Glynn EF, Chen J, Mushegian AR, (2006) Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms. Bioinformatics 22: 310-316.
    • (2006) Bioinformatics , vol.22 , pp. 310-316
    • Glynn, E.F.1    Chen, J.2    Mushegian, A.R.3
  • 19
    • 38649083129 scopus 로고    scopus 로고
    • The plastid sigma factor SIG5 is involved in the diurnal regulation of the chloroplast gene psbD in the moss Physcomitrella patens
    • Ichikawa K, Shimizu A, Okada R, Satbhai SB, Aoki S, (2008) The plastid sigma factor SIG5 is involved in the diurnal regulation of the chloroplast gene psbD in the moss Physcomitrella patens. FEBS Lett 582: 405-409.
    • (2008) FEBS Lett , vol.582 , pp. 405-409
    • Ichikawa, K.1    Shimizu, A.2    Okada, R.3    Satbhai, S.B.4    Aoki, S.5
  • 20
    • 14344266043 scopus 로고    scopus 로고
    • Photoperiod-regulated expression of the PpCOL1 gene encoding a homolog of CO/COL proteins in the moss Physcomitrella patens
    • Shimizu M, Ichikawa K, Aoki S, (2004) Photoperiod-regulated expression of the PpCOL1 gene encoding a homolog of CO/COL proteins in the moss Physcomitrella patens. Biochem Biophys Res Commun 324: 1296-1301.
    • (2004) Biochem Biophys Res Commun , vol.324 , pp. 1296-1301
    • Shimizu, M.1    Ichikawa, K.2    Aoki, S.3
  • 21
    • 76749121417 scopus 로고    scopus 로고
    • Photoperiod-dependent regulation of cell growth by PpCCA1a and PpCCA1b genes encoding single-myb clock proteins in the moss Physcomitrella patens
    • Okada R, Satbhai SB, Aoki S, (2009) Photoperiod-dependent regulation of cell growth by PpCCA1a and PpCCA1b genes encoding single-myb clock proteins in the moss Physcomitrella patens. Genes Genet Syst 84: 379-384.
    • (2009) Genes Genet Syst , vol.84 , pp. 379-384
    • Okada, R.1    Satbhai, S.B.2    Aoki, S.3
  • 22
    • 1042268312 scopus 로고    scopus 로고
    • Circadian expression of the PpLhcb2 gene encoding a major light-harvesting chlorophyll a/b-binding protein in the moss Physcomitrella patens
    • Aoki S, Kato S, Ichikawa K, Shimizu M, (2004) Circadian expression of the PpLhcb2 gene encoding a major light-harvesting chlorophyll a/b-binding protein in the moss Physcomitrella patens. Plant Cell Physiol 45: 68-76.
    • (2004) Plant Cell Physiol , vol.45 , pp. 68-76
    • Aoki, S.1    Kato, S.2    Ichikawa, K.3    Shimizu, M.4
  • 23
    • 33846689706 scopus 로고    scopus 로고
    • Using GOstats to test gene lists for GO term association
    • Falcon S, Gentleman R, (2007) Using GOstats to test gene lists for GO term association. Bioinformatics 23: 257-258.
    • (2007) Bioinformatics , vol.23 , pp. 257-258
    • Falcon, S.1    Gentleman, R.2
  • 24
    • 84860157447 scopus 로고    scopus 로고
    • Transcriptome of protoplasts reprogrammed into stem cells in Physcomitrella patens
    • Xiao L, Zhang L, Yang G, Zhu H, He Y, (2012) Transcriptome of protoplasts reprogrammed into stem cells in Physcomitrella patens. PLoS ONE 7: e35961.
    • (2012) PLoS ONE , vol.7
    • Xiao, L.1    Zhang, L.2    Yang, G.3    Zhu, H.4    He, Y.5
  • 25
    • 77957881755 scopus 로고    scopus 로고
    • Collective dynamics of specific gene ensembles crucial for neutrophil differentiation: the existence of genome vehicles revealed
    • Tsuchiya M, Piras V, Giuliani A, Tomita M, Selvarajoo K, (2010) Collective dynamics of specific gene ensembles crucial for neutrophil differentiation: the existence of genome vehicles revealed. PLoS ONE 5: e12116.
    • (2010) PLoS ONE , vol.5
    • Tsuchiya, M.1    Piras, V.2    Giuliani, A.3    Tomita, M.4    Selvarajoo, K.5
  • 26
    • 34250174230 scopus 로고    scopus 로고
    • An ancient mechanism controls the development of cells with a rooting function in land plants
    • Menand B, Yi K, Jouannic S, Hoffmann L, Ryan E, et al. (2007) An ancient mechanism controls the development of cells with a rooting function in land plants. Science 316: 1477-1480.
    • (2007) Science , vol.316 , pp. 1477-1480
    • Menand, B.1    Yi, K.2    Jouannic, S.3    Hoffmann, L.4    Ryan, E.5
  • 27
    • 0028191458 scopus 로고
    • The rhd6 Mutation of Arabidopsis thaliana Alters Root-Hair Initiation through an Auxin- and Ethylene-Associated Process
    • Masucci JD, (1994) Schiefelbein JW (1994) The rhd6 Mutation of Arabidopsis thaliana Alters Root-Hair Initiation through an Auxin- and Ethylene-Associated Process. Plant Physiol 106: 1335-1346.
    • (1994) Plant Physiol , vol.106 , pp. 1335-1346
    • Masucci, J.D.1    Schiefelbein, J.W.2
  • 28
    • 72149091719 scopus 로고    scopus 로고
    • Microarray analysis of the moss Physcomitrella patens reveals evolutionarily conserved transcriptional regulation of salt stress and abscisic acid signalling
    • Richardt S, Timmerhaus G, Lang D, Qudeimat E, Correa LG, et al. (2010) Microarray analysis of the moss Physcomitrella patens reveals evolutionarily conserved transcriptional regulation of salt stress and abscisic acid signalling. Plant Mol Biol 72: 27-45.
    • (2010) Plant Mol Biol , vol.72 , pp. 27-45
    • Richardt, S.1    Timmerhaus, G.2    Lang, D.3    Qudeimat, E.4    Correa, L.G.5
  • 29
    • 79956295865 scopus 로고    scopus 로고
    • RSL genes are sufficient for rhizoid system development in early diverging land plants
    • Jang G, Yi K, Pires ND, Menand B, Dolan L, (2011) RSL genes are sufficient for rhizoid system development in early diverging land plants. Development 138: 2273-2281.
    • (2011) Development , vol.138 , pp. 2273-2281
    • Jang, G.1    Yi, K.2    Pires, N.D.3    Menand, B.4    Dolan, L.5
  • 30
    • 0037363922 scopus 로고    scopus 로고
    • HES and HERP families: multiple effectors of the Notch signaling pathway
    • Iso T, Kedes L, Hamamori Y, (2003) HES and HERP families: multiple effectors of the Notch signaling pathway. J Cell Physiol 194: 237-255.
    • (2003) J Cell Physiol , vol.194 , pp. 237-255
    • Iso, T.1    Kedes, L.2    Hamamori, Y.3
  • 31
    • 77649179933 scopus 로고    scopus 로고
    • A basic helix-loop-helix transcription factor controls cell growth and size in root hairs
    • Yi K, Menand B, Bell E, Dolan L, (2010) A basic helix-loop-helix transcription factor controls cell growth and size in root hairs. Nat Genet 42: 264-267.
    • (2010) Nat Genet , vol.42 , pp. 264-267
    • Yi, K.1    Menand, B.2    Bell, E.3    Dolan, L.4
  • 32
    • 38849193368 scopus 로고    scopus 로고
    • Regulation of retinal cell fate specification by multiple transcription factors
    • Ohsawa R, Kageyama R, (2008) Regulation of retinal cell fate specification by multiple transcription factors. Brain Res 1192: 90-98.
    • (2008) Brain Res , vol.1192 , pp. 90-98
    • Ohsawa, R.1    Kageyama, R.2
  • 33
    • 37849032457 scopus 로고    scopus 로고
    • The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants
    • Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, et al. (2008) The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science 319: 64-69.
    • (2008) Science , vol.319 , pp. 64-69
    • Rensing, S.A.1    Lang, D.2    Zimmer, A.D.3    Terry, A.4    Salamov, A.5
  • 34
    • 74549148040 scopus 로고    scopus 로고
    • Decomposition of gene expression state space trajectories
    • Mar JC, Quackenbush J, (2009) Decomposition of gene expression state space trajectories. PLoS Comput Biol 5: e1000626.
    • (2009) PLoS Comput Biol , vol.5
    • Mar, J.C.1    Quackenbush, J.2
  • 35
    • 34250359479 scopus 로고    scopus 로고
    • Correlation-maximizing surrogate gene space for visual mining of gene expression patterns in developing barley endosperm tissue
    • Strickert M, Sreenivasulu N, Usadel B, Seiffert U, (2007) Correlation-maximizing surrogate gene space for visual mining of gene expression patterns in developing barley endosperm tissue. BMC Bioinformatics 8: 165.
    • (2007) BMC Bioinformatics , vol.8 , pp. 165
    • Strickert, M.1    Sreenivasulu, N.2    Usadel, B.3    Seiffert, U.4
  • 36
    • 0037900005 scopus 로고    scopus 로고
    • Distributions generated by perturbation of symmetry with emphasis on a multivariate skew-t distribution
    • Azzalini A, Capitanio A, (2003) Distributions generated by perturbation of symmetry with emphasis on a multivariate skew-t distribution. J Roy Statist Soc B 65: 367-389.
    • (2003) J Roy Statist Soc B , vol.65 , pp. 367-389
    • Azzalini, A.1    Capitanio, A.2
  • 38
    • 79960851663 scopus 로고    scopus 로고
    • Why is there a lack of consensus on molecular subgroups of glioblastoma? Understanding the nature of biological and statistical variability in glioblastoma expression data
    • Marko NF, Quackenbush J, Weil RJ, (2011) Why is there a lack of consensus on molecular subgroups of glioblastoma? Understanding the nature of biological and statistical variability in glioblastoma expression data. PLoS ONE 6: e20826.
    • (2011) PLoS ONE , vol.6
    • Marko, N.F.1    Quackenbush, J.2    Weil, R.J.3
  • 39
    • 78049247990 scopus 로고    scopus 로고
    • Combining theoretical analysis and experimental data generation reveals IRF9 as a crucial factor for accelerating interferon alpha-induced early antiviral signalling
    • Maiwald T, Schneider A, Busch H, Sahle S, Gretz N, et al. (2010) Combining theoretical analysis and experimental data generation reveals IRF9 as a crucial factor for accelerating interferon alpha-induced early antiviral signalling. Febs J 277: 4741-4754.
    • (2010) Febs J , vol.277 , pp. 4741-4754
    • Maiwald, T.1    Schneider, A.2    Busch, H.3    Sahle, S.4    Gretz, N.5
  • 40
    • 77958506746 scopus 로고    scopus 로고
    • Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity
    • Lang D, Weiche B, Timmerhaus G, Richardt S, Riano-Pachon DM, et al. (2010) Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol 2: 488-503.
    • (2010) Genome Biol Evol , vol.2 , pp. 488-503
    • Lang, D.1    Weiche, B.2    Timmerhaus, G.3    Richardt, S.4    Riano-Pachon, D.M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.