Public microarray resources

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Nov 8, 2013 (3 years and 7 months ago)

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EMBnet 08.03.2002

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Public microarray resources


DNA Microarrays EMBnet course

Mar. 4
-
8, 2002 ,EMBnet & EPFL,
Lausanne

EMBnet 08.03.2002

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Categories of public
resources


Data repositories sites


Data retrieval sites


On
-
line tools for data analysis


Web supplements to published datasets

EMBnet 08.03.2002

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http://ep.ebi.ac.uk/EP/

Online clustering and analysis tools

http://bioinfo.cnio.es/sotar
ray/

Diverse data analysis tools, very good

http://discover.nci.nih.gov/n
ature2000/natureintromain.
html

Correlations between gene expresison
and pharmacology, data clustering.

http://classify.stanford.edu
/

Expression data classification,
discriminant analysis

http://genebox.ncgr.org/ge
nex/analysis_tools.shtml

Genex analysis tools

http://www.ncbi.nlm.nih.gov
/SAGE/

NCBI SAGE data and analysis (no data
upload)

Web resources : online data upload
and analysis tools

EMBnet 08.03.2002

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http://genome
-
www5.stanford.edu/MicroArray/SMD/

The Stanford Microarray
Database

http://www.informatics.jax.org/mgihome
/GXD/aboutGXD.shtml

Mouse expression data
storage and integration

http://www.cbil.upenn.edu/RAD2/

RNA Abundance Database

http://www.ncbi.nlm.nih.gov/geo/

Gene expression data
repository and online resource

http://www.ebi.ac.uk/arrayexpress/

Public data repository and
public queries

Web resources : public databases

EMBnet 08.03.2002

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http://arep.med.harvard.edu/Expre
ssDB/

Public queries of E. coli and
yeast data

http://genome
-
www4.stanford.edu/cgi
-
bin/SGD/expression/expressionCon
nection.pl

Saccharomyces Genome
Database expression data
retrieval

http://www.transcriptome.ens.fr/y
mgv/

Public queries of yeast data

http://www.cbil.upenn.edu/EpoDB/r
elease/version_2.2/GERD_query.ht
ml

Expression information
retrieval for one gene at a time

Web resources : public databases

EMBnet 08.03.2002

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http://www.hsph.harvard.edu/geneexpre
ssion/

Yeast Transcriptional Profiling
Experiments

http://genome
-
www.stanford.edu/nci60/

Supplement to
Ross et al. (Nat
Genet., 2000).

http://genome
-
www.stanford.edu/serum/

Supplement to Lyer et
al.(1999) Science 283:83
-
87

http://genome
-
www.stanford.edu/breast_cancer/molecu
larportraits/

Supplement to Perou et al.
Nature 406:747
-
752(2000)

http://genome
-
www5.stanford.edu/cgi
-
bin/SMD/listMicroArrayData.pl?tableNa
me=publication

List of papers with links to
their web supplements

Web resources : web supplements

EMBnet 08.03.2002

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http://ihome.cuhk.edu.hk/~b400559/a
rraysoft.html

Link’s page & softwares’ info

http://ep.ebi.ac.uk/Links.html

Expression Profiler link’s page

http://genome
-
www5.stanford.edu/MicroArray/SMD/
resources.html

Stanford's links page, very
complete

Web resources : link’s pages

Today’s exercise

:

Online data analysis and data retrieval