메뉴 건너뛰기




Volumn 38, Issue 1, 2009, Pages

Maximization of negative correlations in time-course gene expression data for enhancing understanding of molecular pathways

Author keywords

[No Author keywords available]

Indexed keywords

LYSINE; TRANSCRIPTION FACTOR;

EID: 75649090766     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp822     Document Type: Article
Times cited : (25)

References (38)
  • 1
    • 0842309161 scopus 로고    scopus 로고
    • Discovering molecular pathways from protein interaction and gene expression data
    • Segal, E., Wang, H. and Koller, D. (2003) Discovering molecular pathways from protein interaction and gene expression data. Bioinformatics, 19(Suppl. 1), i264-i271.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Segal, E.1    Wang, H.2    Koller, D.3
  • 4
    • 27544440058 scopus 로고    scopus 로고
    • Shifting and scaling patterns from gene expression data
    • Aguilar-Ruiz, J.S. (2005) Shifting and scaling patterns from gene expression data. Bioinformatics, 21, 3840-3845.
    • (2005) Bioinformatics , vol.21 , pp. 3840-3845
    • Aguilar-Ruiz, J.S.1
  • 5
    • 0037941585 scopus 로고    scopus 로고
    • Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
    • Segal, E., Shapira, M., Regev, A., Pe'er, D., Botstein, D., Koller, D. and Friedman, N. (2003) Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet., 34, 166-176.
    • (2003) Nat. Genet. , vol.34 , pp. 166-176
    • Segal, E.1    Shapira, M.2    Regev, A.3    Pe'er, D.4    Botstein, D.5    Koller, D.6    Friedman, N.7
  • 6
    • 44349136914 scopus 로고    scopus 로고
    • Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization
    • Cheng, K.O., Law, N.F., Siu, W.C. and Liew, A.W. (2008) Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization. BMC Bioinformatics, 9, 210-237.
    • (2008) BMC Bioinformatics , vol.9 , pp. 210-237
    • Cheng, K.O.1    Law, N.F.2    Siu, W.C.3    Liew, A.W.4
  • 7
    • 38349101892 scopus 로고    scopus 로고
    • Clustering of change patterns using Fourier coefficients
    • Kim, J. and Kim, H. (2008) Clustering of change patterns using Fourier coefficients. Bioinformatics, 24, 184-191.
    • (2008) Bioinformatics , vol.24 , pp. 184-191
    • Kim, J.1    Kim, H.2
  • 9
    • 27644453166 scopus 로고    scopus 로고
    • Microarray analyses of gene expression during chondrocyte differentiation identifies novel regulators of hypertrophy
    • James, C.G., Appleton, C.T., Ulici, V., Underhill, T.M. and Beier, F. (2005) Microarray analyses of gene expression during chondrocyte differentiation identifies novel regulators of hypertrophy. Mol. Biol. Cell, 16, 5316-5333.
    • (2005) Mol. Biol. Cell , vol.16 , pp. 5316-5333
    • James, C.G.1    Appleton, C.T.2    Ulici, V.3    Underhill, T.M.4    Beier, F.5
  • 10
    • 42649110359 scopus 로고    scopus 로고
    • A pattern recognition approach to infer time-lagged genetic interactions
    • Chuang, C.L., Jen, C.H., Chen, C.M. and Shieh, G.S. (2008) A pattern recognition approach to infer time-lagged genetic interactions. Bioinformatics, 24, 1183-1190.
    • (2008) Bioinformatics , vol.24 , pp. 1183-1190
    • Chuang, C.L.1    Jen, C.H.2    Chen, C.M.3    Shieh, G.S.4
  • 11
    • 40649083597 scopus 로고    scopus 로고
    • Strong negative self regulation of prokaryotic transcription factors increases the intrinsic noise of protein expression
    • Stekel, D.J. and Jenkins, D.J. (2008) Strong negative self regulation of prokaryotic transcription factors increases the intrinsic noise of protein expression. BMC Syst. Biol., 2, 6-19.
    • (2008) BMC Syst. Biol. , vol.2 , pp. 6-19
    • Stekel, D.J.1    Jenkins, D.J.2
  • 12
    • 0034079564 scopus 로고    scopus 로고
    • Multiple RAS downstream pathways mediate functional repression of the homeobox gene product ttf-1
    • Missero, C., Pirro, M.T. and Di Lauro, R. (2000) Multiple RAS downstream pathways mediate functional repression of the homeobox gene product ttf-1. Mol. Cell Biol., 20, 2783-2793.
    • (2000) Mol. Cell Biol. , vol.20 , pp. 2783-2793
    • Missero, C.1    Pirro, M.T.2    Di Lauro, R.3
  • 13
    • 34547844125 scopus 로고    scopus 로고
    • Nucleotide variation of regulatory motifs may lead to distinct expression patterns
    • Segal, L., Lapidot, M., Solan, Z., Ruppin, E., Pilpel, Y. and Horn, D. (2007) Nucleotide variation of regulatory motifs may lead to distinct expression patterns. Bioinformatics, 23, i440-i449.
    • (2007) Bioinformatics , vol.23
    • Segal, L.1    Lapidot, M.2    Solan, Z.3    Ruppin, E.4    Pilpel, Y.5    Horn, D.6
  • 14
    • 42149146048 scopus 로고    scopus 로고
    • Inferring transcriptional compensation interactions in yeast via stepwise structure equation modeling
    • Shieh, G.S., Chen, C.M., Yu, C.Y., Huang, J., Wang, W.F. and Lo, Y.C. (2008) Inferring transcriptional compensation interactions in yeast via stepwise structure equation modeling. BMC Bioinformatics, 9, 134-143.
    • (2008) BMC Bioinformatics , vol.9 , pp. 134-143
    • Shieh, G.S.1    Chen, C.M.2    Yu, C.Y.3    Huang, J.4    Wang, W.F.5    Lo, Y.C.6
  • 15
    • 33747609801 scopus 로고    scopus 로고
    • Genome-wide patterns of histone modifications in yeast
    • Millar, C.B. and Grunstein, M. (2006) Genome-wide patterns of histone modifications in yeast. Nat. Rev. Mol. Cell Biol., 7, 657-666.
    • (2006) Nat. Rev. Mol. Cell Biol. , vol.7 , pp. 657-666
    • Millar, C.B.1    Grunstein, M.2
  • 16
    • 33947315736 scopus 로고    scopus 로고
    • Cancer epigenomics: DNA methylomes and histone-modification maps
    • Esteller, M. (2007) Cancer epigenomics: DNA methylomes and histone-modification maps. Nat. Rev. Genet., 8, 286-298.
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 286-298
    • Esteller, M.1
  • 17
    • 42049085369 scopus 로고    scopus 로고
    • Differentially expressed genes are marked by histone 3 lysine 9 trimethylation in human cancer cells
    • Wiencke, J.K., Zheng, S., Morrison, Z. and Yeh, R.F. (2008) Differentially expressed genes are marked by histone 3 lysine 9 trimethylation in human cancer cells. Oncogene, 27, 2412-2421.
    • (2008) Oncogene , vol.27 , pp. 2412-2421
    • Wiencke, J.K.1    Zheng, S.2    Morrison, Z.3    Yeh, R.F.4
  • 19
    • 48549104954 scopus 로고    scopus 로고
    • Partial mixture model for tight clustering of gene expression time-course
    • Yuan, Y., Li, C.T. and Wilson, R. (2008) Partial mixture model for tight clustering of gene expression time-course. BMC Bioinformatics, 9, 287-303.
    • (2008) BMC Bioinformatics , vol.9 , pp. 287-303
    • Yuan, Y.1    Li, C.T.2    Wilson, R.3
  • 20
    • 14644416505 scopus 로고    scopus 로고
    • Identifying time-lagged gene clusters using gene expression data
    • Ji, L. and Tan, K.L. (2005) Identifying time-lagged gene clusters using gene expression data. Bioinformatics, 21, 509-516.
    • (2005) Bioinformatics , vol.21 , pp. 509-516
    • Ji, L.1    Tan, K.L.2
  • 21
    • 35748941236 scopus 로고    scopus 로고
    • Edisa: extracting biclusters from multiple time-series of gene expression profiles
    • Supper, J., Strauch, M., Wanke, D., Harter, K. and Zell, A. (2007) Edisa: extracting biclusters from multiple time-series of gene expression profiles. BMC Bioinformatics, 8, 334-347.
    • (2007) BMC Bioinformatics , vol.8 , pp. 334-347
    • Supper, J.1    Strauch, M.2    Wanke, D.3    Harter, K.4    Zell, A.5
  • 22
    • 76849109141 scopus 로고    scopus 로고
    • Identification of regulatory modules in time series gene expression data using a linear time biclustering algorithm
    • (12 October 2009, date last accessed)
    • Madeira, S.C., Teixeira, M.C., Sá-Correia, I. and Oliveira, A.L. (2008) Identification of regulatory modules in time series gene expression data using a linear time biclustering algorithm. IEEE/ACM Trans. Comput. Biol. Bioinform., 99, http://doi.ieeecomputersociety.org/10.1109/TCBB.2008.34 (12 October 2009, date last accessed).
    • (2008) IEEE/ACM Trans. Comput. Biol. Bioinform. , vol.99
    • Madeira, S.C.1    Teixeira, M.C.2    Sá-Correia, I.3    Oliveira, A.L.4
  • 23
    • 67651018681 scopus 로고    scopus 로고
    • A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series
    • Madeira, S.C. and Oliveira, A.L. (2009) A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series. Alg. Mol. Biol., 4, 8-46.
    • (2009) Alg. Mol. Biol. , vol.4 , pp. 8-46
    • Madeira, S.C.1    Oliveira, A.L.2
  • 24
    • 35649007860 scopus 로고    scopus 로고
    • Maximal biclique subgraphs and closed pattern pairs of the adjacency matrix: a one-to-one correspondence and mining algorithms
    • Li, J., Liu, G., Li, H. and Wong, L. (2007) Maximal biclique subgraphs and closed pattern pairs of the adjacency matrix: a one-to-one correspondence and mining algorithms. IEEE Trans. Knowl. Data Eng., 19, 1625-1637.
    • (2007) IEEE Trans. Knowl. Data Eng. , vol.19 , pp. 1625-1637
    • Li, J.1    Liu, G.2    Li, H.3    Wong, L.4
  • 28
    • 75649124958 scopus 로고    scopus 로고
    • Biggests: integrated environment for biclustering analysis of time series gene expression data
    • Gonalves, J.P., Madeira, S.C. and Oliveira, A.L. (2009) Biggests: integrated environment for biclustering analysis of time series gene expression data. BMC Res. Notes, 2, 124-134.
    • (2009) BMC Res. Notes , vol.2 , pp. 124-134
    • Gonalves, J.P.1    Madeira, S.C.2    Oliveira, A.L.3
  • 29
  • 31
    • 45149101194 scopus 로고    scopus 로고
    • Current approaches to gene regulatory network modelling
    • Schlitt, T. and Brazma, A. (2007) Current approaches to gene regulatory network modelling. BMC Bioinformatics, 8(Suppl. 6), S9.
    • (2007) BMC Bioinformatics , vol.8 , Issue.SUPPL. 6
    • Schlitt, T.1    Brazma, A.2
  • 32
    • 0036578654 scopus 로고    scopus 로고
    • Topological and causal structure of the yeast transcriptional regulatory network
    • Guelzim, N., Bottani, S., Bourgine, P. and Képès, F. (2002) Topological and causal structure of the yeast transcriptional regulatory network. Nat. Genet., 31, 60-63.
    • (2002) Nat. Genet. , vol.31 , pp. 60-63
    • Guelzim, N.1    Bottani, S.2    Bourgine, P.3    Képès, F.4
  • 33
    • 58149333393 scopus 로고    scopus 로고
    • Systematic identification of yeast cell cycle transcription factors using multiple data sources
    • Wu, W.S. and Li, W.H. (2008) Systematic identification of yeast cell cycle transcription factors using multiple data sources. BMC Bioinformatics, 9, 522-534.
    • (2008) BMC Bioinformatics , vol.9 , pp. 522-534
    • Wu, W.S.1    Li, W.H.2
  • 34
    • 1542366496 scopus 로고    scopus 로고
    • Combined overexpression of genes of the ergosterol biosynthetic pathway leads to accumulation of sterols in Saccharomyces cerevisiae
    • Veen, M., Stahl, U. and Lang, C. (2003) Combined overexpression of genes of the ergosterol biosynthetic pathway leads to accumulation of sterols in Saccharomyces cerevisiae. FEMS Yeast Res., 4, 87-95.
    • (2003) FEMS Yeast Res. , vol.4 , pp. 87-95
    • Veen, M.1    Stahl, U.2    Lang, C.3
  • 36
    • 16344389891 scopus 로고    scopus 로고
    • Permutmatrix: a graphical environment to arrange gene expression profiles in optimal linear order
    • Caraux, G. and Pinloche, S. (2005) Permutmatrix: a graphical environment to arrange gene expression profiles in optimal linear order. Bioinformatics, 21, 1280-1281.
    • (2005) Bioinformatics , vol.21 , pp. 1280-1281
    • Caraux, G.1    Pinloche, S.2
  • 37
    • 31044433976 scopus 로고    scopus 로고
    • Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source
    • Ronen, M. and Botstein, D. (2006) Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source. Proc. Natl Acad. Sci. USA, 103, 389-394.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 389-394
    • Ronen, M.1    Botstein, D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.