References
Shields R. MIAME, we have a problem. Trends Genet. 2006 Feb;22(2):65-6. Epub 2005 Dec 27.
PMID: 16380192
Excellent review of the challenges faced when comparing the results of
microarray experiments with the same samples using different platforms in different labs.
Patterson SD, Aebersold RH. Proteomics: the first decade and beyond.Nat
Genet. 2003 Mar;33 Suppl:311-23.Review.
PMID: 12610541
Review of Proteomics--technology, method, objectives and future
co-authored by one of the acknowledged leaders of the field, Dr. Reudi
Aebersold of Seattle's Institute for Systems Biology.
Isogai Y, Tjian R. Targeting genes and transcription factors to segregated
nuclear compartments. Curr Opin Cell Biol. 2003 Jun;15(3):296-303.
PMID: 12787771
Dicussion of current ideas concerning the architecture of cell specific
gene transcription regulation--the arrangement and distribution of
transcription factors in nuclear space is critically important to
differential expression. Reminder that cells are not just "bags of
enzymes".
Levine M, Tjian R. Transcription regulation and animal diversity. Nature.
2003 Jul 10;424(6945):147-51. Review.
PMID: 12853946
Elaboration of the expression paradigm from the evolutionary,
developmental, cellular and molecular perspectives.
Scheel J, Von Brevern MC, Horlein A, Fischer A, Schneider A, Bach A. Yellow
pages to the transcriptome. Pharmacogenomics. 2002 Nov;3(6):791-807. Review.
PMID: 12437481
Detailed review of all current methods used to study
gene expression, with discussion of advantages and
disadvantages of each technology. Also provides information
on the major corporate players in both the methods themselves
and the software necessary for the analysis of expression data.
Thoughtful discussion of future technologies for expression
data acquisition and analysis and consequences for biology
and medicine.
Churchill GA. Fundamentals of experimental design for cDNA microarrays. Nat
Genet. 2002 Dec;32 Suppl:490-5. Review.
PMID: 12454643
Excellent review of proper design and analysis of microarray
experiments, with emphasis on the underlying statistics involved.
Is particularly useful in that it points out the many pitfalls
and fallacies in much of the published microarray work to date,
and how to avoid these problems by careful design.
Stoeckert CJ Jr, Causton HC, Ball CA. Microarray databases: standards and
ontologies. Nat Genet. 2002 Dec;32 Suppl:469-73. Review.
PMID: 12454640
Deals with one of the central issues in microarray
(and indeed all expression research) work-the unbelievable
and unprecedented amounts of data generated even by
relatively simple experiments. Outlines the problems of
how to standardize expression data so that it may be
shared and analyzed by different groups, with emphasis
on the fact that this constitutes a major change for
biology in that, like physics, chemistry and astronomy,
biology must now deal with huge amounts of complex data
requiring computational and statistical methods for
analysis and comprehension.
Quackenbush J. Microarray data normalization and transformation. Nat Genet.
2002 Dec;32 Suppl:496-501. Review.
PMID: 12454644
Thourough description of the problem of microarray data
normalization.
Boon K, Osorio EC, Greenhut SF, Schaefer CF, Shoemaker J, Polyak K, Morin
PJ, Buetow KH, Strausberg RL, De Souza SJ, Riggins GJ. An anatomy of normal
and malignant gene expression. Proc Natl Acad Sci U S A. 2002 Aug
20;99(17):11287-92. Epub 2002 Jul 15.
PMID: 12119410
Beautiful summation of the development of SAGE-Genie,
a powerful set of bioinformatics tools that includes the
SAGE Anatomic Viewer which allows for the simple visual
display of complex gene expression data in the context of
human anatomy and tissue structure.
Barrett JC, Kawasaki ES. Microarrays: the use of oligonucleotides and cDNA
for the analysis of gene expression. Drug Discov Today. 2003 Feb
1;8(3):134-41.
PMID: 12568783
Excellent, very well-written and illustrated review of
current microarray tools for studying gene expression.
Chuaqui RF, Bonner RF, Best CJ, Gillespie JW, Flaig MJ, Hewitt SM, Phillips
JL, Krizman DB, Tangrea MA, Ahram M, Linehan WM, Knezevic V, Emmert-Buck MR.
Post-analysis follow-up and validation of microarray experiments. Nat Genet.
2002 Dec;32 Suppl:509-14. Review.
PMID: 12454646
Discussion of a crucial aspect of expression research-the
validation of microarray generated data by other independent
methods. Is data generated by microarrays biologically meaningful,
and how can we prove it to be so?
Liang P. SAGE Genie: a suite with panoramic view of gene expression. Proc
Natl Acad Sci U S A. 2002 Sep 3;99(18):11547-8.
PMID: 12195021
A thoughtful companion to the Boon et al paper, arguing the
usefulness of SAGE and SAGE Genie over other methods of
expression data acquisition and analysis.
Wheeler DL, Church DM, Federhen S, Lash AE, Madden TL, Pontius JU, Schuler
GD, Schriml LM, Sequeira E, Tatusova TA, Wagner L. Database resources of the
National Center for Biotechnology. Nucleic Acids Res. 2003 Jan
1;31(1):28-33.
PMID: 12519941
Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression
and hybridization array data repository.
Nucleic Acids Res. 2002 Jan 1;30(1):207-10.
PMID: 11752295
Articles summarizing both NCBI databases in general and GEO in
particular.
Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega
RG, Sapinoso LM, Moqrich A, Patapoutian A, Hampton GM, Schultz PG, Hogenesch
JB. Large-scale analysis of the human and mouse transcriptomes. Proc Natl
Acad Sci U S A. 2002 Apr 2;99(7):4465-70. Epub 2002 Mar 19.
PMID: 11904358
Paper describing the generation and analysis of the whole human and
mouse transcriptome datasets with Affymetrix GeneChips published on GEO and
used in this module.
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