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Volumn 4, Issue 4, 2006, Pages 212-229

High-Sensitivity Transcriptome Data Structure and Implications for Analysis and Biologic Interpretation

Author keywords

distribution modeling; microarray analysis; parameter approximation; signal variance distribution; stochastic transcription initiation; transcriptome

Indexed keywords

TRANSCRIPTOME;

EID: 34248664998     PISSN: 16720229     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1672-0229(07)60002-3     Document Type: Article
Times cited : (27)

References (39)
  • 1
    • 0035072249 scopus 로고    scopus 로고
    • Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer
    • Hughes T.R., et al. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 19 (2001) 342-347
    • (2001) Nat. Biotechnol. , vol.19 , pp. 342-347
    • Hughes, T.R.1
  • 2
    • 0347691435 scopus 로고    scopus 로고
    • Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing
    • Castle J., et al. Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing. Genome Biol. 4 (2003) R66
    • (2003) Genome Biol. , vol.4
    • Castle, J.1
  • 3
    • 33747193154 scopus 로고    scopus 로고
    • Performance and bioinformat-ics evaluation of overlapping variable length oligonu-cleotide probes used in spotted microarrays
    • Jordan R., et al. Performance and bioinformat-ics evaluation of overlapping variable length oligonu-cleotide probes used in spotted microarrays. Trans. Integr. Biomed. Inform. Enabl. Technol. Symp. 1 (2004) 15-24
    • (2004) Trans. Integr. Biomed. Inform. Enabl. Technol. Symp. , vol.1 , pp. 15-24
    • Jordan, R.1
  • 4
    • 20344391689 scopus 로고    scopus 로고
    • Regulation of various genes in human leukocytes acutely exposed to morphine: expression microarray analysis
    • Stefano G.B., et al. Regulation of various genes in human leukocytes acutely exposed to morphine: expression microarray analysis. Med. Sci. Monit. 11 (2005) MS35-MS42
    • (2005) Med. Sci. Monit. , vol.11
    • Stefano, G.B.1
  • 5
    • 11144358198 scopus 로고    scopus 로고
    • A gene atlas of the mouse and human protein-encoding transcriptomes
    • Su A.I., et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. USA 101 (2004) 6062-6067
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 6062-6067
    • Su, A.I.1
  • 6
    • 34248652240 scopus 로고    scopus 로고
    • Bilmes, J. A. 1998. A gentle tutorial of the EM algorithm and its appliaction to parameter estimation for Gaussian mixture and hidden Markov models. Technical report, ICSI TR-97-021, University of California at Berkley, USA.
  • 7
    • 34248683504 scopus 로고    scopus 로고
    • Shewchuk, J. R. 1994. An introduction to the conjugate gradient method without the agonizing pain. Technical report, CS-94-125, Carnegie Mellon University, Pittsburgh, USA.
  • 8
    • 2942542735 scopus 로고    scopus 로고
    • Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment
    • Konishi T. Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment. BMC Bioinformatics 5 (2004) 5
    • (2004) BMC Bioinformatics , vol.5 , pp. 5
    • Konishi, T.1
  • 9
    • 0037025618 scopus 로고    scopus 로고
    • Ranking genes with respect to differential expression
    • preprint 0007.
    • Broberg P. Ranking genes with respect to differential expression. Genome Biol. 3 (2002) preprint 0007.
    • (2002) Genome Biol. , vol.3
    • Broberg, P.1
  • 10
    • 25444500666 scopus 로고    scopus 로고
    • Normal uniform mixture differential gene expression detection for cDNA microarrays
    • Dean N., and Raftery A.E. Normal uniform mixture differential gene expression detection for cDNA microarrays. BMC Bioinformatics 6 (2005) 173
    • (2005) BMC Bioinformatics , vol.6 , pp. 173
    • Dean, N.1    Raftery, A.E.2
  • 11
    • 0038053153 scopus 로고    scopus 로고
    • Statistical adjustment of signal censoring in gene expression experiments
    • Wit E., and McClure J. Statistical adjustment of signal censoring in gene expression experiments. Bioinformatics 19 (2003) 1055-1060
    • (2003) Bioinformatics , vol.19 , pp. 1055-1060
    • Wit, E.1    McClure, J.2
  • 12
    • 23344438932 scopus 로고    scopus 로고
    • Scale-freeness and biologic networks
    • Arita M. Scale-freeness and biologic networks. J. Biochem. (Tokyo) 138 (2005) 1-4
    • (2005) J. Biochem. (Tokyo) , vol.138 , pp. 1-4
    • Arita, M.1
  • 13
    • 0038692119 scopus 로고    scopus 로고
    • Human housekeeping genes are compact
    • Eisenberg E., and Levanon E.Y. Human housekeeping genes are compact. Trends Genet. 19 (2003) 362-365
    • (2003) Trends Genet. , vol.19 , pp. 362-365
    • Eisenberg, E.1    Levanon, E.Y.2
  • 14
    • 0037119587 scopus 로고    scopus 로고
    • Stochastic gene expression in a single cell
    • Elowitz M.B., et al. Stochastic gene expression in a single cell. Science 297 (2002) 1183-1186
    • (2002) Science , vol.297 , pp. 1183-1186
    • Elowitz, M.B.1
  • 15
    • 0242416539 scopus 로고    scopus 로고
    • Noise in eukaryotic gene expression
    • Blake W.J., et al. Noise in eukaryotic gene expression. Nature 422 (2003) 633-637
    • (2003) Nature , vol.422 , pp. 633-637
    • Blake, W.J.1
  • 16
    • 2942718723 scopus 로고    scopus 로고
    • Control of stochasticity in eukaryotic gene expression
    • Raser J.M., and O'Shea E.K. Control of stochasticity in eukaryotic gene expression. Science 304 (2004) 1811-1814
    • (2004) Science , vol.304 , pp. 1811-1814
    • Raser, J.M.1    O'Shea, E.K.2
  • 17
    • 12144261863 scopus 로고    scopus 로고
    • Self-organization vs Watchmaker: stochastic gene expression and cell differentiation
    • Kurakin A. Self-organization vs Watchmaker: stochastic gene expression and cell differentiation. Dev. Genes Evol. 215 (2005) 46-52
    • (2005) Dev. Genes Evol. , vol.215 , pp. 46-52
    • Kurakin, A.1
  • 18
    • 29244462834 scopus 로고    scopus 로고
    • Transcriptional stochastic-ity in gene expression
    • Lipniacki T., et al. Transcriptional stochastic-ity in gene expression. J. Theor. Biol. 238 (2006) 348-367
    • (2006) J. Theor. Biol. , vol.238 , pp. 348-367
    • Lipniacki, T.1
  • 19
    • 19544379881 scopus 로고    scopus 로고
    • Stochasticity in gene expression: from theories to phenotypes
    • Kaern M., et al. Stochasticity in gene expression: from theories to phenotypes. Nat. Rev. Genet. 6 (2005) 451-464
    • (2005) Nat. Rev. Genet. , vol.6 , pp. 451-464
    • Kaern, M.1
  • 20
    • 10044260032 scopus 로고    scopus 로고
    • Modeling and simulation of 228 Geno. Prot. Bioinfo. biological systems with stochasticity
    • Meng T.C., et al. Modeling and simulation of 228 Geno. Prot. Bioinfo. biological systems with stochasticity. In Silico Biol. 4 (2004) 293-309
    • (2004) In Silico Biol. , vol.4 , pp. 293-309
    • Meng, T.C.1
  • 21
    • 6344284947 scopus 로고    scopus 로고
    • DEMSIM: a discrete event based mechanistic simulation platform for gene expression and regulation dynamics
    • Dasika M.S., et al. DEMSIM: a discrete event based mechanistic simulation platform for gene expression and regulation dynamics. J. Theor. Biol. 232 (2005) 55-69
    • (2005) J. Theor. Biol. , vol.232 , pp. 55-69
    • Dasika, M.S.1
  • 22
    • 33645317935 scopus 로고    scopus 로고
    • Genomic plasticity and information processing by transcription coregulators
    • Benecke A. Genomic plasticity and information processing by transcription coregulators. Complexus 1 (2003) 65-76
    • (2003) Complexus , vol.1 , pp. 65-76
    • Benecke, A.1
  • 23
    • 33645285263 scopus 로고    scopus 로고
    • Chromatin code, local non-equilibrium dynamics, and the emergence of transcription regulatory programs
    • Benecke A. Chromatin code, local non-equilibrium dynamics, and the emergence of transcription regulatory programs. Eur. Phys. J. E (Soft Matter) 19 (2006) 353-366
    • (2006) Eur. Phys. J. E (Soft Matter) , vol.19 , pp. 353-366
    • Benecke, A.1
  • 24
    • 33747330684 scopus 로고    scopus 로고
    • Normalization using weighted negative second order exponential error functions (NeONORM) provides robustness against asymmetries in comparative transcriptome profiles and avoids false calls
    • Noth S., et al. Normalization using weighted negative second order exponential error functions (NeONORM) provides robustness against asymmetries in comparative transcriptome profiles and avoids false calls. Genomics Proteomics Bioinformatics 4 (2006) 90-109
    • (2006) Genomics Proteomics Bioinformatics , vol.4 , pp. 90-109
    • Noth, S.1
  • 25
    • 84936916896 scopus 로고
    • Robust locally weighted regression and smoothing scatterplots
    • Cleveland W.S. Robust locally weighted regression and smoothing scatterplots. J. Amer. Statist. Assoc. 74 (1979) 829-836
    • (1979) J. Amer. Statist. Assoc. , vol.74 , pp. 829-836
    • Cleveland, W.S.1
  • 26
    • 84947318637 scopus 로고
    • Locally weighted regression: an approach to regression analysis by local fitting
    • Cleveland W.S., and Devlin S. Locally weighted regression: an approach to regression analysis by local fitting. J. Amer. Statist. Assoc. 83 (1988) 596-610
    • (1988) J. Amer. Statist. Assoc. , vol.83 , pp. 596-610
    • Cleveland, W.S.1    Devlin, S.2
  • 27
    • 13244289933 scopus 로고    scopus 로고
    • Optimized LOWESS normalization parameter selection for DNA microarray data
    • Berger J.A., et al. Optimized LOWESS normalization parameter selection for DNA microarray data. BMC Bioinformatics 5 (2004) 194
    • (2004) BMC Bioinformatics , vol.5 , pp. 194
    • Berger, J.A.1
  • 28
    • 0242317346 scopus 로고    scopus 로고
    • Fundamentals of cDNA microarray data analysis
    • Leung Y.F., and Cavalieri D. Fundamentals of cDNA microarray data analysis. Trends Genet. 19 (2003) 649-659
    • (2003) Trends Genet. , vol.19 , pp. 649-659
    • Leung, Y.F.1    Cavalieri, D.2
  • 29
    • 12244284624 scopus 로고    scopus 로고
    • DNA microarray experiments: biological and technological aspects
    • Nguyen D.V., et al. DNA microarray experiments: biological and technological aspects. Biometrics 58 (2002) 701-717
    • (2002) Biometrics , vol.58 , pp. 701-717
    • Nguyen, D.V.1
  • 30
    • 84984933234 scopus 로고    scopus 로고
    • High density synthetic oligonucleotide arrays
    • Lipschutz R.J., et al. High density synthetic oligonucleotide arrays. Nat. Genet. 21 (1999) 20-24
    • (1999) Nat. Genet. , vol.21 , pp. 20-24
    • Lipschutz, R.J.1
  • 31
    • 0034927555 scopus 로고    scopus 로고
    • Analysis of variance for gene expression microarray data
    • Kerr M.K., et al. Analysis of variance for gene expression microarray data. J. Comput. Biol. 7 (2000) 819-837
    • (2000) J. Comput. Biol. , vol.7 , pp. 819-837
    • Kerr, M.K.1
  • 32
    • 13244284649 scopus 로고    scopus 로고
    • Rank Difference Analysis of Microarrays (RDAM), a novel approach to statistical analysis of microarray expression profiling data
    • Martin D.E., et al. Rank Difference Analysis of Microarrays (RDAM), a novel approach to statistical analysis of microarray expression profiling data. BMC Bioinformatics 5 (2004) 148
    • (2004) BMC Bioinformatics , vol.5 , pp. 148
    • Martin, D.E.1
  • 33
    • 0035999977 scopus 로고    scopus 로고
    • A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments
    • Pan W. A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. Bioinformatics 18 (2002) 546-554
    • (2002) Bioinformatics , vol.18 , pp. 546-554
    • Pan, W.1
  • 34
    • 0034954414 scopus 로고    scopus 로고
    • Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks
    • Khan J., et al. Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat. Med. 7 (2001) 673-679
    • (2001) Nat. Med. , vol.7 , pp. 673-679
    • Khan, J.1
  • 35
    • 13444282534 scopus 로고    scopus 로고
    • Outcome signature genes in breast cancer: is there a unique set?
    • Ein-Dor L., et al. Outcome signature genes in breast cancer: is there a unique set?. Bioinformatics 21 (2005) 171-178
    • (2005) Bioinformatics , vol.21 , pp. 171-178
    • Ein-Dor, L.1
  • 36
    • 32544449970 scopus 로고    scopus 로고
    • Thermodynamics of RNA/DNA hybridization in high density oligonu-cleotide microarrays
    • Carlon E., and Heim T. Thermodynamics of RNA/DNA hybridization in high density oligonu-cleotide microarrays. Physica A 362 (2006) 433-449
    • (2006) Physica A , vol.362 , pp. 433-449
    • Carlon, E.1    Heim, T.2
  • 37
    • 18244384210 scopus 로고    scopus 로고
    • Multiple-laboratory comparison of microarray platforms
    • Irizarry R.A., et al. Multiple-laboratory comparison of microarray platforms. Nat. Methods. 2 (2005) 345-350
    • (2005) Nat. Methods. , vol.2 , pp. 345-350
    • Irizarry, R.A.1
  • 38
    • 13444304325 scopus 로고    scopus 로고
    • NCBI GEO: mining millions of expression profiles-database and tools
    • Barrett T., et al. NCBI GEO: mining millions of expression profiles-database and tools. Nucleic Acids Res. 33 (2005) D562-D566
    • (2005) Nucleic Acids Res. , vol.33
    • Barrett, T.1
  • 39
    • 30044442305 scopus 로고    scopus 로고
    • Avoiding inconsistencies over time and tracking difficulties in Applied Biosystems AB1700™/Panther™ probe-to-gene annotations
    • Noth S., and Benecke A. Avoiding inconsistencies over time and tracking difficulties in Applied Biosystems AB1700™/Panther™ probe-to-gene annotations. BMC Bioinformatics 6 (2005) 307
    • (2005) BMC Bioinformatics , vol.6 , pp. 307
    • Noth, S.1    Benecke, A.2


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