Litteraturoversikt
for statistikere: mikormatriser
Azadeh Badiee, 2002
(♣ anbefales)
History on differential expression
analysis:
Lee MLT, Kuo FC, Whitmore GA and Sklar J
(2000), Importance of replication in microarray gene expression studies:
Statistical methods and evidence from repetitive cDNA hybridizations.
Proceedings of the National Academy of Sciences, 97(18):9834-9838.
Chen Y, Dougherty ER, and Bittner ML (1997), Ratio-based
decisions and the quantitative
analysis of cDNA microarray images. Journal of Biomedical Optics, 2(4):364-374.
Sapir M and Churchill GA (2000), Estimating
the posterior probability of differential gene,expression from microarray data.
Poster, The Jackson Laboratory,
http://www.jax.org/research/churchill/pubs/marina.pdf
♣ Newton MA,
Kendziorski CM, Richmond CS, Blattner FR and Tsui KW (2001),
On differential variability of expression ratios: improving statistical
inference about gene expression changes from microarray data. Journal of
Computational Biology, 8(1):37-52.
http://www.biostat.wisc.edu/geda/eba.html
Roberts CJ, Nelson B, Marton MJ, Stoughton S,
Meyer MR, Bennet HA,
He YD, Dai H, Walker WL, Hughes TR, Tyers M,
Boone C, and Friend SH (2000),
Singnaling and circuitry of multiple mapk
pathways revealed by a matrix of global gene expression. Science, 287:873.
Normalization and T-statistic:
♣♣
Dudoit S, Yang YH, Callow MJ, and
Speed TP (2001), Statistical methods for identifying differentially
expressed genes in replicated cDNA microarray experiments.
Berkeley Tech Report #578.
http://www.stat.berkeley.edu/users/terry/zarray/Html/papersindex.html
♣♣ Yang YH, Dudoit S, Luu P and Speed TP (2001), Normalization for cDNA
microarray Data. Berkeley Tech Report #589. http://www.stat.berkeley.edu/users/terry/zarray/Html/papersindex.html
Yang YH,
Dudoit, S, Luu P, Lin DM, Peng V, Ngai J and Speed TP (2002), Normalization
for cDNA microarray Data: a robust composite methode addressing single and
multiple slide systematic variation. Nucleic Acid Research, 8(4) e15.
ANOVA and Experimental design:
Kerr MK, Martin M,
Churchill GA (2000),
Analysis of variance for gene expression microarray data. Journal of
Computational Biology, 7:819-837.
♣ Kerr MK and
Churchill GA(2001), Statistical design and the analysis of gene expression
microarrays. Genet
Res. 2001 Apr;77(2):123-8.
♣ Kerr MK and Churchill GA (2001), Experimental
design for gene expression microarrays. Biostatistics, in press.
http://www.jax.org/research/churchill/pubs/index.html
Kerr MK, Leiter EH and Churchill GA
(2001), Analysis of a designed microarray experiment. Proceedings
of the IEEE-Eurasip Nonlinear Signal and Image Processing Workshop. http://www.jax.org/research/churchill/pubs/index.html
♣♣ Kerr
MK, Afshari CA, Bennett L, Bushel P, Martinez J, Walker NJ and Churchill GA
(2001), Statistical analysis of a gene expression microarray experiment with
replication. Statistica Sinica, to appear.
http://www.jax.org/research/churchill/pubs/index.html
Wei Jin,
Rebecca M. Riley, Russell D. Wolfinger, Kevin P. White, Gisele Passador-Gurgel,
Greg Gibson (2001), The contributions of sex, genotype and age to
transcriptional variance in Drosophila melanogaster. Nature Genetics, 29: 389 – 395.
Churchill GA
and Oliver B (2001), Sex,
flies and microarrays.
Nature Genetics, 29: 355 – 356.
Pavlidis P, Noble WS
(2001), Analysis of strain and regional variation in gene expression in
mouse brain. Genome Biology, 2(10): research0042.1-0042.15.
♣ Thomas JG, Olson JM, Tapscott SJ, Zhao LP (2001), An efficient and robust statistical modeling
approach to discover differentially expressed genes using genomic expression
profiles. Genome Res. 2001
Jul;11(7):1227-36. (Olignucleotide).
Bayesian:
♣♣ Efron B,
Tibshirani R and Tusher V (2001), Empirical bayes analysis of a microarray
experiment. Journal of the American statistical association, 96(456):
1151-1160.
Tusher V, Tibshirani R
and Chu G (2001), Significance analysis of microarrays applied to transcriptional
response to ionizing radiation. Proceedings of the National Academy of
Sciences, 98(9):5116-5121.
♣♣ Lonnstedt I
and Speed TP (2001), Replicated microarray data. Statistical Sinica, in
press.
♣ Baldi P, Long AD
(2001), A Bayesian framework for the analysis of microarray expression data:
regularized t-test and statistical inferences of gene changes. Bioinformatics,
17:509-519.
Long AD, Mangalam HJ, Chan BY, Tolleri L, Hatfield GW, Baldi P (2001), Improved statistical inference from DNA
microarray data using analysis of variance and a Bayesian statistical
framework. Analysis of global gene expression in Escherichia coli K12. J Biol Chem,
8;276(23):19937-44.
Error models/intensity-based:
♣ Rocke D, Durbin B (2001), A model for
measurement error for gene expression arrays.
Journal of Computational Biology, 8(6):557-569.
♣♣ Ideker T,
Thorsson V, Siegel AF, Hood LE (2000), Testing for differentially-expressed
genes by maximum-likelihood analysis of microarray data. Journal of
Computational Biology, 7(6):805-818.
Kamb A and Ramaswami M (2001), A simple method for statistical analysis of intensity differences in
microarray-derived gene expression data. BMC
Biotechnol, 1(8).
♣ Chilingaryan A,
Gevorgyan N, Vardanyan A, Jones D, Szabo A (2002), Multivariate approach for selecting sets of
differentially expressed genes.
Math
Biosci, 176(1):59-69.
Miscellaneous:
Tseng GC, Oh MK,
Rohlin L, Liao JC and Wong WH(2001), Issues in cDNA microarray analysis:
quality filtering, channel normalization, models of variation and assessment of
gene effects. Nucleic Acids Research, 29(12):2549-2557.
Yue H, Eastman PS, Wang BB, Minor J, Doctolero MH, Nuttall RL, Stack R,
Becker JW, Montgomery JR, Vainer M, Johnston R (2001), An evaluation of the performance of cDNA
microarrays for detecting changes in global mRNA expression. Nucleic Acids Res,
29(8):E41-1.
JM Claverie (1999), Computational
methods for the identification of differential and coordinated gene expression.
Human Molecular Genetics, 8(10):1821-1832.
♣ Yang MC, Ruan QG,
Yang JJ, Eckenrode S, Wu S, McIndoe RA, She JX.
Physiol Genomics (2001), A statistical procedure for flagging weak spots
greatly improves normalization and ratio estimates in microarray experiments.
Physiol. Genomics, in pres.
Johannes Schuchhardt,
Dieter Beule, Arif Malik, Eryc Wolski, Holger Eickhoff, Hans Lehrach and
Hanspeter Herzel (2000), Normalization strategies for cDNA microarrays.
(NAR methods online), Nucleic Acids Research,28(10):E47.
Jindan Yu, Mohammad I.
Othman, Rafal Farjo, Sepideh Zareparsi, Sean P. MacNee, Shigeo Yoshida, Anand
Swaroop (2002), Technical Brief: Evaluation and optimization of procedures for target
labeling and hybridization of cDNA microarrays. Molecular vision,
8:130-137.
From
http://www.bioconductor.org/:
♣♣ Dudoit
and Gentleman: Introduction to
genome biology and microarray experiments
Dudoit and
Gentleman: cDNA microarray
experiments: pre-processing and experimental design.
♣♣ Carey and
Gentleman: Working with
multiple microarrays.
♣♣ Dudoit
and Gentleman: Classification
in microarray experiments.
From NTNU:
♣ Mette Langaas: Overall assessment of differentially
expressed genes using FDR and FNR.
♣ Per Kristian
Lehre: Analysis of microarray
data GCR-meeting, NTNU.
Introduction
to microarrays:
M. Schena, D. Shalon,
R. Davis and P. Brown (1995), Quantitative monitoring of gene expression
patterns with a complementary DNA microarray. Science, 270 5235, p. 467.
J. DeRisi, L. Penland,
P.O. Brown, M.L. Bittner, P.S. Meltzer, M. Ray, Y. Chen, Y.A. Su and J.M. Trent
(1996), Use of a cDNA microarray to analyse gene expression patterns in
human cancer. Nature Genet, 14(4):
457.
M. Schena, D. Shalon,
R. Heller, A. Chai, P. Brown and R. Davis (1996), Parallel human genome
analysis: microarray-based expression monitoring of 1000 genes. Proc. Nat.
Acad. Sci. USA 93(20):
10614.
P Brown, D Bostein
(1999), Exploring the new world of the genome with DNA microarrays.
Nature Genetics, 21(1 suppl):33-37.
Clustering / Networks / Patterns /
Profiling / Data mining:
Kjersti Aas (2001),
Microarray data mining: A survey. Note, Norsk
Regnesentral, SAMBA/02/01.
B Dysvik, I Jonassen
(2001), J_Express: exploring gene expression data using Java. Bioinformatics,
17:369-370.
Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T,
Eisen MB, van de Rijn M, Jeffrey SS, Thorsen T, Quist H, Matese JC, Brown PO,
Botstein D, Eystein Lonning P, Borresen-Dale AL (2001), Gene expression patterns of breast carcinomas
distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci, 11;98(19):10869-74.
Toshihisa Takagi
(2000), Inferring genetic networks from DNA microarray data by multiple
regression analysis. Genome Informatics, 11:118-128.
Not read yet: (har ikke lest disse
ennå, men har planer om det:-)
Sorin Draghici, Alexander Kuklin, Bruce Hoff
& Soheil Shams (2001), Experimental design, analysis of variance and
slide quality assessment in gene expression arrays. Current Opinion in Drug
Discovery & Development, 4(3):332-337
Mark J van der Lann, Jenny Bryan (2001), Gene
expression analysis with the parametric bootstrap. Biostatistics, in press.
J Theilhaber, S Bushnell, A Jackson, R Fuchs
(2001), Bayesian estimation of fold-changes in the analysis of gene
expression: the PFOLD algorithm. Journal of Computational Biology,
8(6):585-614.
Jeffrey G Thomas, James M Olson, Stephen J
Tapscott, Lue Ping Zhao (2001), An efficient and robust statistical modeling
approach to discover differentially expressed genes using genomic expression
profiles. Genome Research, 11:1227-1236.
S Datta (2001), Exploring relationships in
gene expressions: A partial least squares approach. Gene Expression, to
appear.
Thomas JG, Olson JM, Tapscott SJ, Zhao LP
(2001), An efficient and robust statistical modeling approach to discover
differentially expressed genes using genomic expression profiles. Genome
Res, 11(7), 1227-36.
DM Mutch, A Berger, R Mansourian, A Rytz, MA Roberts (2001), Microarray data
analysis: a practical approach for selecting differentially expressed genes.
Genome Biology, 2(12):preprint0009.
PJ Park, M Pagano, and M Bonetti (2001), A
nonparametric scoring algorithm for identifying informative genes from
microarray data. PSB01, 6:52-63.
N Friedman, M Linial, I Nachman, D Pe'er
(2000), Using Bayesian networks to analyze expression data. Journal of
Computational Biology, 7(3/4):601-620.
Orly Alter, Patrick O Brown, David Botstein
(2000), Singular value decomposition for genome-wide expression data processing
and modeling. Proceedings of the National Academy of Sciences,
97(18):10101-10106.
Michael E Wall, Patricia A Dyck, Thomas S
Brettin (2001), SVDMAN - singular value decomposition analysis of microarray
data. Bioinformatics, 17:566-568.
Xuhua Xia, Zheng Xie (2001), AMADA: analysis
of microarray data. Bioinformatics, 17(6):569-590.
MPS Brown, WN Grundy,
D Lin, C Sugnet, M Ares, Jr. D Haussler (2000), Knowledge-based analysis of
microarray gene expression data by using support vector machines.
Proceedings of the National Academy of Sciences, 97:262-267.
TR Hvidsten, J Komorowski, AK Sandvik, and A
Lægreid (2001), Predicting gene function from gene expressions and
ontologies. PSB01, 6:299-310.
M Xiong, L Jin, W Li,
E Boerwinkle (2000), Computational methods for gene expression-based tumor
classification. Biotechniques, 29(6):1264-1268.
E van Someren, LFA
Wessels, MJT Reinders (2000), Linear modeling of genetic networks from
experimental data. ISMB'00.
A Zien, R Kuffner, R
Zimmer, T Lengauer (2000), Analysis of gene expression data with pathway
scores. ISMB'00.
I. Hedenfalk, D. Duggan, Y. Chen, M. Radmacher,
M. Bittner, R. Simon, P. Meltzer, B. Gusterson, M. Esteller, O.P. Kallioniemi,
B. Wilfond, A. Borg and J. Trent (2001), Gene-expression profiles in hereditary
breast cancer. New England J. Med., 344
(8): 539.