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Fetching data from publications
In this exercise we get ourselves familiar with the process of
obtaining data that could be used for modeling biological
networks. We will not focus on the databases, but instead
study on what kind of public data sets have been presented
and analyzed in recent high-level publications. In this
exercise we will not analyze the data sets, but the data
available in these publications can be used later in the
project work.
Below is a list of articles that all describe or use publicly
accessible data. Pick 2-4 of them, quickly read the relevant
sections of the papers to see
what kind of data they have analyzed, and then proceed
to find the data in the web. Some of the data files are
small, and you should then download them in order to take
a look, while some are so big that we cannot right now
download them.
Write down a few observations from each of the papers you
chose. An example could be something like: "PPI data from
baker's yeast, obtained using mass spectrometry. Contains
X interactions (binary values) between Y proteins. The
data is stored in a tab-delimited file, which looks easy
to parse." You can also write down what they did with the
data in the paper.
Publications
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Nevan J Krogan et al. 2006 Global landscape of protein complexes in the
yeast Saccharomyces cerevisiae. Nature. 2006 Mar 30; 440: 637-643
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Anne-Claude Gavin et al. 2006 Proteome survey reveals modularity of the
yeast cell machinery. Nature. 2006 Mar 30; 440: 631-636
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Schwikowski,B., Uetz,P. & Fields,S. (2000) A network of protein-protein
interactions in yeast. Nature Biotechnology 18 (12): 1257-1261
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Uetz P, et al. A comprehensive analysis of protein-protein interactions in
Saccharomyces cerevisiae. Nature. 2000 Feb 10;403(6770):623-7.
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Yuen Ho et al. Systematic identification of protein complexes in
Saccharomyces cerevisiae by mass spectrometry. 2002. Nature 415, 180-183 (10
January 2002)
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Titz, B. et al. 2004. What do we learn from high-throughput protein
interaction data and networks? Expert Reviews in Proteomics 1 (1): 89-99
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Nizar N Batada et al. Stratus Not Altocumulus: A New View of the Yeast
Protein Interaction Network. PLoS Biol. 2006 Sep 19;4 (10).
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Sean R Collins et al. 2007 Towards a comprehensive atlas of the physical
interactome of Saccharomyces cerevisiae. Mol Cell Proteomics. 2007 Jan 2.
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Rob M Ewing et al. 2007 Large-scale mapping of human protein-protein
interactions by mass spectrometry. Mol Syst Biol. 2007 ; 3: 89. Epub 2007
Mar 13.
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Ganghi et al. 2006. Analysis of the human protein interactome and comparison
with yeast, worm and fly interaction datasets. Nature genetics 38: 285-293.
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Ptacek et al. 2005. Global analysis of protein phosphorylation in yeast. Nature
438: 679-684.
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Tong et al. 2004. Global mapping of the yeast genetic interaction network. Science 303: 808-813.
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Ghaemmaghami et al. Global analysis of protein expression in yeast. Nature 425:
737-741
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Ihmels et al. Principles of transcriptional control in the metabolic network of
Saccharomyces cerevisiae. 2004 Nature Biotechnology 22: 86-92
Some of the data is likely to be in the general
databases. Here are links to few of those. Even if
the articles you chose did not link to these, you should
take a brief look at what each has to offer.
"Solutions" to the exercise
-
Yeast PPI data in form of link propabilities,
found in supplementary material
-
Nobody was interested...
-
Yeast PPI data in binary form, collected from several
sources
-
Yeast PPI data; no downloadable version was found, only
a web interface for individual interactions
-
Nobody was interested...
-
Fruit fly PPI data, binary, easily obtained from DIP database
-
Yeast PPI data, binary, in supplementary information
-
Yeast PPI data, likelihoods of interactions, uses previous data
-
Nobody was interested...
-
Data from protein chips, distributed as excel-files
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Yeast data in a pdf-file, needs heavy parsing
-
Yeast proteome data, easy to obtain in plain text and from
database
-
Expression and network data for yeast, compiled from
several sources and the combination is not available
Wireless internet access
The accounts you received can be used for authentication in the Aalto
wireless network, which should work in most places in Otaniemi. See
Aalto web page for
instructions. Essentially you only need to set the net password
using "passwd" in the unix command shell. You can also use the same
command to change the master password, but make sure you don't
forget the new one.
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last updated Wednesday, 15-Aug-2007 14:49:05 EEST