Vertical and Horizontal Approaches: Hypothesis-driven research concentrates on one protein and uses many different tools for its characterization. We refer to the vertical arrow as the ''vertical approach.'' Large-scale functional genomics experiments - PowerPoint PPT Presentation

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Vertical and Horizontal Approaches: Hypothesis-driven research concentrates on one protein and uses many different tools for its characterization. We refer to the vertical arrow as the ''vertical approach.'' Large-scale functional genomics experiments

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Title: Vertical and Horizontal Approaches: Hypothesis-driven research concentrates on one protein and uses many different tools for its characterization. We refer to the vertical arrow as the ''vertical approach.'' Large-scale functional genomics experiments


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Vertical and Horizontal Approaches
Hypothesis-driven research concentrates on one
protein and uses many different tools for its
characterization. We refer to the vertical arrow
as the ''vertical approach.'' Large-scale
functional genomics experiments apply the same
tool to many if not all genes or proteins. We
refer to the horizontal arrow as the ''horizontal
approach.' A Biological Atlas of Functional
Maps, Marc Vidal, Cell, Vol 104, 333-339, 2001
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in silico interaction prediction
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Phylogenetic profile method
Matteo Pellegrini et al., Assigning protein
functions by comparative genome analysis
Proteinphylogenetic profiles, PNAS 96 4285-4288,
1999
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The Rosetta Stone method
Detecting Protein Function and Protein-Protein
Interactions from Genome Sequences , Edward M.
Marcotte et al., Science, 285, 751-753, 1999
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Proteomics to study genes and genomes Akhilesh
Pandey and Matthias Mann Nature405, 837 - 846,
2000
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??? nuclear pore ( NPC nuclear pore
complex )
Rout, M. P. and Aitchison, J. D. (2001). The
Nuclear Pore Complex as a Transport Machine. J.
Biol. Chem. 276 16593-16596
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Michael P. Rout et al., The Yeast Nuclear Pore
Complex Composition, Architecture, and Transport
Mechanism J. Cell Biol. 2000 148 635-652
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Proteomics to study genes and genomes Akhilesh
Pandey and Matthias Mann Nature405, 837 - 846,
2000
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Anuj Kumar et al., Subcellular localization of
the yeast proteome Genes Dev. 2002 16 707-719.
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Proteomics to study genes and genomes Akhilesh
Pandey and Matthias Mann Nature405, 837 - 846,
2000
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A network of protein-protein interactions in
yeast Benno Schwikowski, Peter Uetz, Stanley
Fields Nature Biotechnology18, 1257 - 1261, 2000
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Random 12-mers fused to a minor coat protein
(pIII) of M13
Epitope mapping with Ph.D.-12
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Protein-fold evolution in the test tube,
Christiane Schaffitzel and Andreas Plukthun,
Trends in Biochemical Sciences 26, 577-579,2001
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Mass spectrometry from genomics to proteomics,
Yates, J. R., III, Trends in Genetics, 16, 5-8,
2000
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Molecular Cloning A Laboratory Manual, 3rd
edition, Sambrook, J. and Russel,D. W.
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Functional organization of the yeast proteome by
systematic analysis of protein complexes,
Anne-claude Gavin et al., Nature 415, 141 - 147
(2002)
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Molecular Biology of the Cell, 4th edition,
Alberts, B. et al.
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Identification of in vivo substrates of the
chaperonin GroEL Walid A. Houry, Dmitrij
Frishman, Christoph Eckerskorn, Friedrich
Lottspeich, F. Ulrich Hartl, Nature402, 147 -
154, 1999
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Comparative assessment of large-scale data sets
of proteinprotein interactions , CHRISTIAN VON
MERING et al., Nature 417, 399 - 403 (2002)
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Comparative assessment of large-scale data sets
of proteinprotein interactions , CHRISTIAN VON
MERING et al., Nature 417, 399 - 403 (2002)
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Integration of Functional Maps An example is
shown for C. elegans. By integrating several
large-scale functional genomic projects it should
be possible to formulate increasingly meaningful
hypotheses A Biological Atlas of Functional Maps,
Marc Vidal, Cell, Vol 104, 333-339, 2001
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An Atlas of Functional Maps Conceptually, each
''ome'' map can be conceived as a two-dimensional
matrix. The X axis represents the genome, the
complete set of ORFs (ORFeome see Walhout et
al., 2000b ), or the proteome. The Y axis
represents a set of conditions, genetic
backgrounds or phenotypes, or even the proteome
itself (see text for details). Overlapping maps
in the Z axis constitute the biological atlas A
Biological Atlas of Functional Maps, Marc Vidal,
Cell, Vol 104, 333-339, 2001
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