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Volumn 6, Issue 3, 2008, Pages 493-519

Using directed information to build biologically relevant influence networks

Author keywords

Comparative genomics; Directed information; Mutual information; Transcription factor module; Transcription regulatory network

Indexed keywords

TRANSCRIPTION FACTOR;

EID: 46049101230     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720008003515     Document Type: Conference Paper
Times cited : (21)

References (53)
  • 3
    • 15944426084 scopus 로고    scopus 로고
    • Bayesian analysis of signaling networks governing embryonic stem cell fate decisions
    • Woolf PJ, Prudhomme W, Daheron L, Daley GQ, Lauffenburger DA, Bayesian analysis of signaling networks governing embryonic stem cell fate decisions, Bioinformatics 21(6):741-753, 2005.
    • (2005) Bioinformatics , vol.21 , Issue.6 , pp. 741-753
    • Woolf, P.J.1    Prudhomme, W.2    Daheron, L.3    Daley, G.Q.4    Lauffenburger, D.A.5
  • 4
    • 0015737911 scopus 로고
    • The bidirectional communication theory - A generalization of information theory
    • Marko H, The bidirectional communication theory - A generalization of information theory, IEEE Trans Commun 21:1345-1351, 1973.
    • (1973) IEEE Trans Commun , vol.21 , pp. 1345-1351
    • Marko, H.1
  • 6
    • 34249819354 scopus 로고    scopus 로고
    • Source coding with feed-forward: Rate-distortion theorems and error exponents for a general source
    • Venkataramanan R, Pradhan SS, Source coding with feed-forward: Rate-distortion theorems and error exponents for a general source, IEEE Trans Inf Theory 53(6):2154-2179, 2007.
    • (2007) IEEE Trans Inf Theory , vol.53 , Issue.6 , pp. 2154-2179
    • Venkataramanan, R.1    Pradhan, S.S.2
  • 7
    • 84894912254 scopus 로고
    • The measurement of linear dependence and feedback between multiple time series
    • With comments by Parzen E, Pierce DA, Wei W, Zellner A, and rejoinder
    • Geweke J, The measurement of linear dependence and feedback between multiple time series, J Am Stat Assoc 77:304-324, 1982. (With comments by Parzen E, Pierce DA, Wei W, Zellner A, and rejoinder)
    • (1982) J Am Stat Assoc , vol.77 , pp. 304-324
    • Geweke, J.1
  • 9
    • 33748696278 scopus 로고    scopus 로고
    • Information theory, multivariate dependence, and genetic network inference
    • Technical Report NSF-KITP-04-54, Kavli Institute for Theoretical Physics, University of California at Santa Barbara, Santa Barbara, CA
    • Nemenman I, Information theory, multivariate dependence, and genetic network inference, Technical Report NSF-KITP-04-54, Kavli Institute for Theoretical Physics, University of California at Santa Barbara, Santa Barbara, CA, 2004.
    • (2004)
    • Nemenman, I.1
  • 10
    • 8644243022 scopus 로고    scopus 로고
    • Multiple, distant Gata2 enhancers specify temporally and tissue-specific patterning in the developing urogenital system
    • Khandekar M, Suzuki N, Lewton J, Yamamoto M, Engel JD, Multiple, distant Gata2 enhancers specify temporally and tissue-specific patterning in the developing urogenital system, Mol Cell Biol 24 23):10263-10276, 2004.
    • (2004) Mol Cell Biol , vol.24 , Issue.23 , pp. 10263-10276
    • Khandekar, M.1    Suzuki, N.2    Lewton, J.3    Yamamoto, M.4    Engel, J.D.5
  • 11
    • 33646229522 scopus 로고    scopus 로고
    • Practical strategies for discovering regulatory DNA sequence motifs
    • MacIsaac KD, Fraenkel E, Practical strategies for discovering regulatory DNA sequence motifs, PLoS Comput Biol 2(4):e36, 2006.
    • (2006) PLoS Comput Biol , vol.2 , Issue.4
    • MacIsaac, K.D.1    Fraenkel, E.2
  • 12
    • 3042731990 scopus 로고    scopus 로고
    • Identification of sparsely distributed clusters of cis regulatory elements in sets of co-expressed genes
    • Kreiman G, Identification of sparsely distributed clusters of cis regulatory elements in sets of co-expressed genes, Nucleic Acids Res 32(9):2889-2900, 2004.
    • (2004) Nucleic Acids Res , vol.32 , Issue.9 , pp. 2889-2900
    • Kreiman, G.1
  • 13
    • 0032938120 scopus 로고    scopus 로고
    • Localization of distant urogenital system-, central nervous system-, and endocardium-specific transcriptional regulatory elements in the GATA-3 locus
    • Lakshmanan G, Lieuw KH, Lim KC, Gu Y, Grosveld F, Engel JD, Karis A, Localization of distant urogenital system-, central nervous system-, and endocardium-specific transcriptional regulatory elements in the GATA-3 locus, Mol Cell Biol 19(2):1558-1568, 1999.
    • (1999) Mol Cell Biol , vol.19 , Issue.2 , pp. 1558-1568
    • Lakshmanan, G.1    Lieuw, K.H.2    Lim, K.C.3    Gu, Y.4    Grosveld, F.5    Engel, J.D.6    Karis, A.7
  • 19
    • 84898931392 scopus 로고    scopus 로고
    • Entropy and inference, revisited
    • Dietterich TG, Becker S, Ghahramani Z eds, MIT Press, Cambridge, MA
    • Nemenman I, Shafee F, Bialek W, Entropy and inference, revisited, in Dietterich TG, Becker S, Ghahramani Z (eds.), Advances in Neural Information Processing Systems, Vol. 14, MIT Press, Cambridge, MA, 2002.
    • (2002) Advances in Neural Information Processing Systems , vol.14
    • Nemenman, I.1    Shafee, F.2    Bialek, W.3
  • 20
    • 0041877169 scopus 로고    scopus 로고
    • Estimation of entropy and mutual information
    • Paninski L, Estimation of entropy and mutual information, Neural Comput 15:1191-1254, 2003.
    • (2003) Neural Comput , vol.15 , pp. 1191-1254
    • Paninski, L.1
  • 22
    • 46049100697 scopus 로고    scopus 로고
    • Learned-Miller E, Hyperspacings and the estimation of information theoretic quantities, Technical Report 04-104, University of Massachusetts Amherst, Amherst, MA, 2004.
    • Learned-Miller E, Hyperspacings and the estimation of information theoretic quantities, Technical Report 04-104, University of Massachusetts Amherst, Amherst, MA, 2004.
  • 25
    • 0003568656 scopus 로고    scopus 로고
    • Moonen CTW, Bandettini PA eds, Springer, Berlin
    • Moonen CTW, Bandettini PA (eds.), Functional MRI, Springer, Berlin, 2000.
    • (2000) Functional MRI
  • 26
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y, Controlling the false discovery rate: A practical and powerful approach to multiple testing, J R Stat Soc Ser B 57:289-300, 1995.
    • (1995) J R Stat Soc Ser B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 27
    • 15944364151 scopus 로고    scopus 로고
    • An empirical Bayes approach to inferring large-scale gene association networks
    • Schäfer J, Strimmer K, An empirical Bayes approach to inferring large-scale gene association networks, Bioinformatics 21 754-764, 2005.
    • (2005) Bioinformatics , vol.21 , pp. 754-764
    • Schäfer, J.1    Strimmer, K.2
  • 29
    • 13844253637 scopus 로고    scopus 로고
    • A Bayesian approach to reconstructing genetic regulatory networks with hidden factors
    • Beal MJ, Falciani F, Ghahramani Z, Rangel C, Wild DL, A Bayesian approach to reconstructing genetic regulatory networks with hidden factors, Bioinformatics 21(3):349-356, 2005.
    • (2005) Bioinformatics , vol.21 , Issue.3 , pp. 349-356
    • Beal, M.J.1    Falciani, F.2    Ghahramani, Z.3    Rangel, C.4    Wild, D.L.5
  • 31
    • 34247188062 scopus 로고    scopus 로고
    • Analysis of gene coexpression by B-spline based CoD estimation
    • Li H, Sun Y, Zhan M, Analysis of gene coexpression by B-spline based CoD estimation, EURASIP J Bioinform Syst Biol 2007:6, 2007.
    • (2007) EURASIP J Bioinform Syst Biol , vol.6 , pp. 2007
    • Li, H.1    Sun, Y.2    Zhan, M.3
  • 32
    • 0036847229 scopus 로고    scopus 로고
    • Gene expression regulation by retinoic acid
    • Balmer JE, Blomhoff R, Gene expression regulation by retinoic acid, J Lipid Res 43(11):1773-1808, 2002.
    • (2002) J Lipid Res , vol.43 , Issue.11 , pp. 1773-1808
    • Balmer, J.E.1    Blomhoff, R.2
  • 33
    • 31644438184 scopus 로고    scopus 로고
    • Pax 2/8-regulated Gata3 expression is necessary for morphogenesis and guidance of the nephric duct in the developing kidney
    • Grote D, Souabni A, Busslinger M, Bouchard M, Pax 2/8-regulated Gata3 expression is necessary for morphogenesis and guidance of the nephric duct in the developing kidney, Development 133(1):53-61, 2006.
    • (2006) Development , vol.133 , Issue.1 , pp. 53-61
    • Grote, D.1    Souabni, A.2    Busslinger, M.3    Bouchard, M.4
  • 34
    • 2542495011 scopus 로고    scopus 로고
    • Angiotensin II increases Pax-2 expression in fetal kidney cells via the AT2 receptor
    • Zhang SL, Moini B, Ingelfinger JR, Angiotensin II increases Pax-2 expression in fetal kidney cells via the AT2 receptor, J Am Soc Nephrol 15(6):1452-1465, 2004.
    • (2004) J Am Soc Nephrol , vol.15 , Issue.6 , pp. 1452-1465
    • Zhang, S.L.1    Moini, B.2    Ingelfinger, J.R.3
  • 35
    • 16844373321 scopus 로고    scopus 로고
    • Ezzat S, Mader R, Yu S, Ning T, Poussier P, Asa SL, Ikaros integrates endocrine and immune system development, J Clin Invest 115 4:844-848, 2005.
    • Ezzat S, Mader R, Yu S, Ning T, Poussier P, Asa SL, Ikaros integrates endocrine and immune system development, J Clin Invest 115 4):844-848, 2005.
  • 36
    • 0032531605 scopus 로고    scopus 로고
    • Differential responsiveness of the IL-5 and IL-4 genes to transcription factor GATA-3
    • Zhang DH, Yang L, Ray A, Differential responsiveness of the IL-5 and IL-4 genes to transcription factor GATA-3, J Immunol 161 3817-3821, 1998.
    • (1998) J Immunol , vol.161 , pp. 3817-3821
    • Zhang, D.H.1    Yang, L.2    Ray, A.3
  • 39
    • 23644436149 scopus 로고    scopus 로고
    • Computational identification of regulatory DNAs underlying animal development
    • Papatsenko D, Levine M, Computational identification of regulatory DNAs underlying animal development, Nat Methods 2:529-534, 2005.
    • (2005) Nat Methods , vol.2 , pp. 529-534
    • Papatsenko, D.1    Levine, M.2
  • 41
    • 0344514713 scopus 로고    scopus 로고
    • Changes in gene expression patterns in the ureteric bud and metanephric mesenchyme in models of kidney development
    • Stuart RO, Bush KT, Nigam SK, Changes in gene expression patterns in the ureteric bud and metanephric mesenchyme in models of kidney development, Kidney Int 64(6):1997-2008, 2003.
    • (2003) Kidney Int , vol.64 , Issue.6 , pp. 1997-2008
    • Stuart, R.O.1    Bush, K.T.2    Nigam, S.K.3
  • 42
    • 0026601176 scopus 로고
    • Pax-2 is a DNA-binding protein expressed in embryonic kidney and Wilms tumor
    • Dressler GR, Douglas EC, Pax-2 is a DNA-binding protein expressed in embryonic kidney and Wilms tumor, Proc Natl Acad Sci USA 89 1179-1183, 1992.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 1179-1183
    • Dressler, G.R.1    Douglas, E.C.2
  • 45
    • 0028021033 scopus 로고
    • Characterization of the mouse HNF-4 gene and its expression during mouse embryogenesis
    • Taraviras S, Monaghan AP, Schtz G, Kelsey G, Characterization of the mouse HNF-4 gene and its expression during mouse embryogenesis, Mech Dev 48(2):67-79, 1994.
    • (1994) Mech Dev , vol.48 , Issue.2 , pp. 67-79
    • Taraviras, S.1    Monaghan, A.P.2    Schtz, G.3    Kelsey, G.4
  • 48
    • 0043172526 scopus 로고    scopus 로고
    • Wnt11 and Ret/ Gdnf pathways cooperate in regulating ureteric branching during metanephric kidney development
    • Majumdar A, Vainio S, Kispert A, McMahon J, McMahon AP, Wnt11 and Ret/ Gdnf pathways cooperate in regulating ureteric branching during metanephric kidney development, Development 130 14):3175-3185, 2003.
    • (2003) Development , vol.130 , Issue.14 , pp. 3175-3185
    • Majumdar, A.1    Vainio, S.2    Kispert, A.3    McMahon, J.4    McMahon, A.P.5
  • 49
    • 0035044372 scopus 로고    scopus 로고
    • Intracellular and extracellular regulation of ureteric bud morphogenesis
    • Davies J, Intracellular and extracellular regulation of ureteric bud morphogenesis, J Anat 198(3):257-264, 2001.
    • (2001) J Anat , vol.198 , Issue.3 , pp. 257-264
    • Davies, J.1
  • 51
    • 0035215311 scopus 로고    scopus 로고
    • Regulation of ureteric bud outgrowth by Pax2-dependent activation of the glial derived neurotrophic factor gene
    • Brophy PD, Ostrom L, Lang KM, Dressler GR, Regulation of ureteric bud outgrowth by Pax2-dependent activation of the glial derived neurotrophic factor gene, Development 128(23):4747-4756, 2001.
    • (2001) Development , vol.128 , Issue.23 , pp. 4747-4756
    • Brophy, P.D.1    Ostrom, L.2    Lang, K.M.3    Dressler, G.R.4
  • 53
    • 68349153730 scopus 로고
    • Relative entropy measures of multivariate dependence
    • Joe H, Relative entropy measures of multivariate dependence, J Am Stat Assoc 84:157-164, 1989.
    • (1989) J Am Stat Assoc , vol.84 , pp. 157-164
    • Joe, H.1


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