메뉴 건너뛰기




Volumn 7, Issue 3, 2003, Pages 235-252

PAINT: A Promoter Analysis and Interaction Network Generation Tool for Gene Regulatory Network Identification

Author keywords

[No Author keywords available]

Indexed keywords

1 (4 DIMETHYLAMINO 3 METHYLBENZYL) 5 DIPHENYLACETYL 4,5,6,7 TETRAHYDRO 1H IMIDAZO[4,5 C]PYRIDINE 6 CARBOXYLIC ACID; ANGIOTENSIN; ANGIOTENSIN RECEPTOR; NEUROPEPTIDE; TRANSCRIPTION FACTOR;

EID: 0142074896     PISSN: 15362310     EISSN: None     Source Type: Journal    
DOI: 10.1089/153623103322452378     Document Type: Article
Times cited : (114)

References (54)
  • 3
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • Menlo Park, California
    • BAILEY, T.L., and ELKAN, C. (1994). Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Presented at the Second International Conference on Intelligent Systems in Molecular Biology, Menlo Park, California. Available: http://meme.sdsc.edu/meme/website/.
    • (1994) Second International Conference on Intelligent Systems in Molecular Biology
    • Bailey, T.L.1    Elkan, C.2
  • 4
    • 0033970466 scopus 로고    scopus 로고
    • Regulation of neurogenesis by interactions between HEN1 and neuronal LMO proteins
    • BAO, J., TALMAGE, D.A., ROLE, L.W., et al. (2000). Regulation of neurogenesis by interactions between HEN1 and neuronal LMO proteins. Development 127, 425-435.
    • (2000) Development , vol.127 , pp. 425-435
    • Bao, J.1    Talmage, D.A.2    Role, L.W.3
  • 6
    • 0037154273 scopus 로고    scopus 로고
    • Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome
    • BERMAN, B.P., NIBU, Y., PFEIFFER, B.D., et al. (2002). Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proceedings of the National Academy of Science USA 99, 757-762.
    • (2002) Proceedings of the National Academy of Science USA , vol.99 , pp. 757-762
    • Berman, B.P.1    Nibu, Y.2    Pfeiffer, B.D.3
  • 10
    • 0035661318 scopus 로고    scopus 로고
    • Angiotensin II promotes the phosphorylation of cyclic AMP-responsive element binding protein (CREB) at Ser133 through an ERK1/2-dependent mechanism
    • CAMMAROTA, M., BEVILAQUA, L.R., DUNKLEY, P.R., et al. (2001). Angiotensin II promotes the phosphorylation of cyclic AMP-responsive element binding protein (CREB) at Ser133 through an ERK1/2-dependent mechanism. Journal of Neurochemistry 79, 1122-1128.
    • (2001) Journal of Neurochemistry , vol.79 , pp. 1122-1128
    • Cammarota, M.1    Bevilaqua, L.R.2    Dunkley, P.R.3
  • 11
    • 0032612220 scopus 로고    scopus 로고
    • Linear modeling of mRNA expression levels during CNS development and injury
    • D'HAESELEER, P., WEN, X., FUHRMAN, S., et al. (1999). Linear modeling of mRNA expression levels during CNS development and injury. Pacific Symposium on Biocomputing 4, 41-52.
    • (1999) Pacific Symposium on Biocomputing , vol.4 , pp. 41-52
    • D'Haeseleer, P.1    Wen, X.2    Fuhrman, S.3
  • 12
    • 0036500609 scopus 로고    scopus 로고
    • A Genomic regulatory network for development
    • DAVIDSON, E.H., RAST, J.P., OLIVERI, P., et al. (2002). A Genomic regulatory network for development. Science 295, 1669-1678.
    • (2002) Science , vol.295 , pp. 1669-1678
    • Davidson, E.H.1    Rast, J.P.2    Oliveri, P.3
  • 13
    • 0035735265 scopus 로고    scopus 로고
    • Computational identification of promoters and first exons in the human genome
    • DAVULURI, R.V., GROSSE, I., and ZHANG, M.Q. (2001). Computational identification of promoters and first exons in the human genome. Nature Genetics 29, 412.
    • (2001) Nature Genetics , vol.29 , pp. 412
    • Davuluri, R.V.1    Grosse, I.2    Zhang, M.Q.3
  • 14
    • 0030933977 scopus 로고    scopus 로고
    • Conservation of the Notch signalling pathway in mammalian neurogenesis
    • DE LA POMPA, J.L., WAKEHAM, A., CORREIA, K.M., et al. (1997). Conservation of the Notch signalling pathway in mammalian neurogenesis. Development 124, 1139-1148.
    • (1997) Development , vol.124 , pp. 1139-1148
    • Pompa, D.E.L.A.1    Wakeham, J.L.2    Correia, A.3
  • 15
    • 0029281048 scopus 로고
    • Protein-DNA interactions during phenotypic differentiation
    • DOBI, A.L., PALKOVITS, M., PALKOVITS, C.G., et al. (1995). Protein-DNA interactions during phenotypic differentiation. Molecular Neurobiology 10, 185-203.
    • (1995) Molecular Neurobiology , vol.10 , pp. 185-203
    • Dobi, A.L.1    Palkovits, M.2    Palkovits, C.G.3
  • 17
    • 0038444122 scopus 로고    scopus 로고
    • Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells
    • ELKON, R., LINHART, C., SHARAN, R., et al. (2003). Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Research 13, 773-780.
    • (2003) Genome Research , vol.13 , pp. 773-780
    • Elkon, R.1    Linhart, C.2    Sharan, R.3
  • 18
    • 0036366689 scopus 로고    scopus 로고
    • Combining location and expression data for principled discovery of genetic regulatory network models
    • HARTEMINK, J., GIFFORD, D.K., JAAKOLA, T.S., et al. (2002). Combining location and expression data for principled discovery of genetic regulatory network models. Pacific Symposium on Biocomputing 7, 437-449.
    • (2002) Pacific Symposium on Biocomputing , vol.7 , pp. 437-449
    • Hartemink, J.1    Gifford, D.K.2    Jaakola, T.S.3
  • 19
    • 0032567081 scopus 로고    scopus 로고
    • Dissecting the regulatory circuitry of a eukaryotic genome
    • HOLSTEGE, F.C., JENNINGS, E.G., WYRICK, J.J., et al. (1998). Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95, 717-728.
    • (1998) Cell , vol.95 , pp. 717-728
    • Holstege, F.C.1    Jennings, E.G.2    Wyrick, J.J.3
  • 21
    • 0002980018 scopus 로고    scopus 로고
    • The ERATO Systems Biology Workbench: An integrated environment for multiscale and multitheoretic simulations in systems biology
    • Kitano, H. (ed) (MIT Press, Cambridge, MA)
    • HUCKA, M., FINNEY, A., SAURO, H., et al. (2001). The ERATO Systems Biology Workbench: an integrated environment for multiscale and multitheoretic simulations in systems biology. In: Kitano, H. (ed). Foundations in System Biology (MIT Press, Cambridge, MA), pgs 125-143.
    • (2001) Foundations in System Biology , pp. 125-143
    • Hucka, M.1    Finney, A.2    Sauro, H.3
  • 22
    • 0034628901 scopus 로고    scopus 로고
    • Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
    • HUGHES, J.D., ESTEP, P.W., TAVAZOIE, S., et al. (2000). Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. Journal of Molecular Biology 296, 1205-1214.
    • (2000) Journal of Molecular Biology , vol.296 , pp. 1205-1214
    • Hughes, J.D.1    Estep, P.W.2    Tavazoie, S.3
  • 23
    • 0000801240 scopus 로고    scopus 로고
    • Discovering regulatory and signalling circuits in molecular interaction networks
    • IDEKER, T., OZIER, O., SCHWIKOWSKI, B., et al. (2002). Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18, S233-S240.
    • (2002) Bioinformatics , vol.18
    • Ideker, T.1    Ozier, O.2    Schwikowski, B.3
  • 24
    • 0035805255 scopus 로고    scopus 로고
    • Integrated genomic and proteomic analyses of a systematically perturbed metabolic network
    • IDEKER, T., THORSSON, V., RANISH, J.A., et al. (2001). Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292, 929.
    • (2001) Science , vol.292 , pp. 929
    • Ideker, T.1    Thorsson, V.2    Ranish, J.A.3
  • 25
    • 0028809646 scopus 로고
    • DNA binding through distinct domains of zinc-finger-homeodomain protein AREB6 has different effects on gene transcription
    • IKEDA, K., and KAWAKAMI, K. (1995). DNA binding through distinct domains of zinc-finger-homeodomain protein AREB6 has different effects on gene transcription. European Journal of Biochemistry 233, 73.
    • (1995) European Journal of Biochemistry , vol.233 , pp. 73
    • Ikeda, K.1    Kawakami, K.2
  • 26
    • 0035156258 scopus 로고    scopus 로고
    • Assessing clusters and motifs from gene expression data
    • JAKT, L.M., CAO, L., CHEAH, K.S., et al. (2001). Assessing clusters and motifs from gene expression data. Genome Research 11, 112-123.
    • (2001) Genome Research , vol.11 , pp. 112-123
    • Jakt, L.M.1    Cao, L.2    Cheah, K.S.3
  • 27
    • 0035825662 scopus 로고    scopus 로고
    • Functional annotaiion of a full-length mouse cDNA collection
    • KAWAI, J., SHINAGAWA, A., SHIBATA, K., et al. (2001). Functional annotaiion of a full-length mouse cDNA collection. Nature 409, 685.
    • (2001) Nature , vol.409 , pp. 685
    • Kawai, J.1    Shinagawa, A.2    Shibata, K.3
  • 28
    • 0028896690 scopus 로고
    • Angiotensin II induces a complex activation of transcription factors in the rat brain: Expression of Fos, Jun and Krox proteins
    • LEBRUN, C.J., BLUME, A., HERDEGEN, T., et al. (1995). Angiotensin II induces a complex activation of transcription factors in the rat brain: expression of Fos, Jun and Krox proteins. Neuroscience. 65, 93-99.
    • (1995) Neuroscience , vol.65 , pp. 93-99
    • Lebrun, C.J.1    Blume, A.2    Herdegen, T.3
  • 29
    • 0037095744 scopus 로고    scopus 로고
    • Combining chromatin immunoprecipitation and DNA footprinting: A novel method to analyze protein-DNA interactions in vivo
    • KANG, L.S.H., VIEIRA, K., and BUNGERT, J. (2002). Combining chromatin immunoprecipitation and DNA footprinting: a novel method to analyze protein-DNA interactions in vivo. Nucleic Acids Research 30, e44.
    • (2002) Nucleic Acids Research , vol.30
    • Kang, L.S.H.1    Vieira, K.2    Bungert, J.3
  • 30
    • 0036124446 scopus 로고    scopus 로고
    • Consensus promoter identification in the human genome utilizing expressed gene markers and gene modeling
    • LIU, R., and STATES, D.J. (2002). Consensus promoter identification in the human genome utilizing expressed gene markers and gene modeling. Genome Research 12, 462-469.
    • (2002) Genome Research , vol.12 , pp. 462-469
    • Liu, R.1    States, D.J.2
  • 31
    • 0033777916 scopus 로고    scopus 로고
    • The role of Jak/STAT signaling in heart tissue renin-angiotensin system
    • MASCARENO, E., and SIDDIQUI, M.A. (2000). The role of Jak/STAT signaling in heart tissue renin-angiotensin system. Molecular Cell Biochememistry 212, 171-175.
    • (2000) Molecular Cell Biochememistry , vol.212 , pp. 171-175
    • Mascareno, E.1    Siddiqui, M.A.2
  • 32
    • 0037174670 scopus 로고    scopus 로고
    • Network motifs: Simple building blocks of complex networks
    • MILO, R., SHEN-ORR, S., ITZKOVITZ, S., et al. (2002). Network motifs: simple building blocks of complex networks. Science 298, 823-827.
    • (2002) Science , vol.298 , pp. 823-827
    • Milo, R.1    Shen-Orr, S.2    Itzkovitz, S.3
  • 33
    • 0028347522 scopus 로고
    • Characterization of the DNA-binding properties of the myeloid zinc finger protein MZF1: Two independent DNA-binding domains recognize two DNA consensus sequences with a common G-rich core
    • MORRIS, J.F., HROMAS, R., and RAUSCHER, F.J. (1994) Characterization of the DNA-binding properties of the myeloid zinc finger protein MZF1: two independent DNA-binding domains recognize two DNA consensus sequences with a common G-rich core. Molecular Cell Biology 14, 1786.
    • (1994) Molecular Cell Biology , vol.14 , pp. 1786
    • Morris, J.F.1    Hromas, R.2    Rauscher, F.J.3
  • 34
    • 0033564126 scopus 로고    scopus 로고
    • Expression and genetic interaction of transcription factors GATA-2 and GATA-3 during development of the mouse central nervous system
    • NARDELLI, J., THIESSON, D., FUJIWARA, Y., et al. (1999). Expression and genetic interaction of transcription factors GATA-2 and GATA-3 during development of the mouse central nervous system. Developmental Biology 210, 305-321.
    • (1999) Developmental Biology , vol.210 , pp. 305-321
    • Nardelli, J.1    Thiesson, D.2    Fujiwara, Y.3
  • 35
    • 0033563512 scopus 로고    scopus 로고
    • The biology of eukaryotic promoter prediction - A review
    • PEDERSEN, A.G., BALDI, P., CHAUVIN, Y., et al. (1999). The biology of eukaryotic promoter prediction - a review. Computers & Chemistry 23, 191-207.
    • (1999) Computers & Chemistry , vol.23 , pp. 191-207
    • Pedersen, A.G.1    Baldi, P.2    Chauvin, Y.3
  • 36
    • 0035957967 scopus 로고    scopus 로고
    • Identification and characterization of a novel nuclear factor of activated T-cells 1 isoform expressed in mouse brain
    • PLYTE, S., BONCRISTIANO, M., FATTORI, E., et al. (2001). Identification and characterization of a novel nuclear factor of activated T-cells 1 isoform expressed in mouse brain. Journal of Biological Chemistry 276, 14350-14358.
    • (2001) Journal of Biological Chemistry , vol.276 , pp. 14350-14358
    • Plyte, S.1    Boncristiano, M.2    Fattori, E.3
  • 37
    • 0028971143 scopus 로고
    • MatInd and MatInspector - New fast and versatile tools for detection of consensus matches in nucleotide sequence data
    • QUANDT, K., FRECH, K., KARAS, H., et al. (1995). MatInd and MatInspector - new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Research 23, 4878. Available: www.genomatix.de.
    • (1995) Nucleic Acids Research , vol.23 , pp. 4878
    • Quandt, K.1    Frech, K.2    Karas, H.3
  • 38
    • 0034814071 scopus 로고    scopus 로고
    • Control motifs for intracellular regulatory networks
    • RAO, C.V., and ARKIN, A.P. (2001). Control motifs for intracellular regulatory networks. Annual Review Biomedical Engineering 3, 391-419.
    • (2001) Annual Review Biomedical Engineering , vol.3 , pp. 391-419
    • Rao, C.V.1    Arkin, A.P.2
  • 40
    • 0025343603 scopus 로고
    • The use of cultured cells in the study of mood-normalizing drugs
    • RACHELSON, E. (1990). The use of cultured cells in the study of mood-normalizing drugs. Pharmacological Toxicology 66, Suppl: 3, 69-75.
    • (1990) Pharmacological Toxicology , vol.66 , Issue.SUPPL. 3 , pp. 69-75
    • Rachelson, E.1
  • 41
    • 0036678794 scopus 로고    scopus 로고
    • Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics
    • RONEN, M., ROSENBERG, R., SHRAIMAN, B.I., et al. (2002). Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proceedings of the National Academy of Science USA 99, 10555-10560.
    • (2002) Proceedings of the National Academy of Science USA , vol.99 , pp. 10555-10560
    • Ronen, M.1    Rosenberg, R.2    Shraiman, B.I.3
  • 43
    • 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., et al. (2003). Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nature Genetics 34, 166-176.
    • (2003) Nature Genetics , vol.34 , pp. 166-176
    • Segal, E.1    Shapira, M.2    Regev, A.3
  • 44
    • 0033028596 scopus 로고    scopus 로고
    • Systematic determination of genetic network architecture
    • TAVAZOIE, S., HUGHES, J.D., CAMPBELL, M.J., et al. (1999). Systematic determination of genetic network architecture. Nature Genetics 22, 281-285.
    • (1999) Nature Genetics , vol.22 , pp. 281-285
    • Tavazoie, S.1    Hughes, J.D.2    Campbell, M.J.3
  • 45
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology
    • THE GENE ONTOLOGY CONSORTIUM. (2000). Gene ontology: tool for the unification of biology. Nature Genetics 25, 25-29.
    • (2000) Nature Genetics , vol.25 , pp. 25-29
  • 47
    • 85039629262 scopus 로고    scopus 로고
    • UCSC GENOME BROWSER. (2003). Available: http://genome.ucsc.edu.
    • (2003)
  • 48
    • 0036024957 scopus 로고    scopus 로고
    • Characterizing transcription factor binding sites using formaldehyde crosslinking and immunoprecipitation
    • WELLS, J., and FARNHAM, P.J. (2002). Characterizing transcription factor binding sites using formaldehyde crosslinking and immunoprecipitation. Methods 26, 48-56.
    • (2002) Methods , vol.26 , pp. 48-56
    • Wells, J.1    Farnham, P.J.2
  • 50
    • 0035172256 scopus 로고    scopus 로고
    • The TRANSFAC system on gene expression regulation
    • WINGENDER, E., CHEN, X., FRICKE, E., et al. (2001). The TRANSFAC system on gene expression regulation. Nucleic Acids Research 29, 281.
    • (2001) Nucleic Acids Research , vol.29 , pp. 281
    • Wingender, E.1    Chen, X.2    Fricke, E.3
  • 51
    • 0036104265 scopus 로고    scopus 로고
    • Angiotensin II activates nuclear transcription factor-kappaB through AT1 and AT2 receptors
    • WOLF, G., WENZEL, U., BURNS, K.D., et al. (2002). Angiotensin II activates nuclear transcription factor-kappaB through AT1 and AT2 receptors. Kidney International 61, 1986-1995.
    • (2002) Kidney International , vol.61 , pp. 1986-1995
    • Wolf, G.1    Wenzel, U.2    Burns, K.D.3
  • 52
    • 0037148909 scopus 로고    scopus 로고
    • The LIM-domain protein Lmo2 is a key regulator of tumour angiogenesis: A new anti-angiogenesis drug target
    • YAMADA, Y., PANNELL, R., FORSTER, A., et al. (2002). The LIM-domain protein Lmo2 is a key regulator of tumour angiogenesis: a new anti-angiogenesis drug target. Oncogene 21, 1309-1315.
    • (2002) Oncogene , vol.21 , pp. 1309-1315
    • Yamada, Y.1    Pannell, R.2    Forster, A.3
  • 53
    • 0037197936 scopus 로고    scopus 로고
    • Reverse engineering gene networks using singular value decomposition and robust regression
    • YEUNG, M.K., TEGNER, J., and COLLINS, J.J. (2002). Reverse engineering gene networks using singular value decomposition and robust regression. Proceedings of the National Academy of Science USA 99, 6163-6168.
    • (2002) Proceedings of the National Academy of Science USA , vol.99 , pp. 6163-6168
    • Yeung, M.K.1    Tegner, J.2    Collins, J.J.3
  • 54
    • 0242651270 scopus 로고    scopus 로고
    • Simulation studies for the identification of genetic networks from cDNA array and regulatory activity data
    • ZAK, D.E., DOYLE, F.J., GONYE, G.E., et al. (2001). Simulation studies for the identification of genetic networks from cDNA array and regulatory activity data. Presented at the Second International Conference on Systems Biology.
    • (2001) Second International Conference on Systems Biology
    • Zak, D.E.1    Doyle, F.J.2    Gonye, G.E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.