Microarray Bioinformatics

Abstract

Bioinformatics covers the application of computational tools for expanding the use of biological, medical or health‐related data. This includes tools to handle, acquire, store, organize, archive, analyse or visualize data.

Keywords: bioinformatics; gene expression analysis; patient stratification; molecular diagnostics; microarray; data analysis

Figure 1.

Linking clinical data with molecular data. Correlation view of specimens from 285 patients with AML showing an adapted correlation view (2856 probe sets). The correlation displays pairwise correlations between the samples. The colours of the cells relate to Pearson's correlation coefficient values, with deeper colours indicating higher positive (red) or negative (blue) correlations.

Figure 2.

The OmniViz data‐mining software is used here to integrate dynamic analyses of multiple data sources. The microarray analysis (upper left) identifies novel, unforeseen relationships, but deciding which of the behaviours is worth pursuing requires further data. In this case, the microarray analysis is linked with investigation of protein expression (upper right), analysis of structures and high‐throughput screening of compounds known to interact with related targets (lower left) and contextual analysis of the vast scientific literature (lower right). Through visualizing and automatic linking of these analyses simultaneously, it is possible to define which line of investigation will be more fruitful from both a scientific and business perspective.

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Web Links

Affymetrix http://www.affymetrix.com/index.affx

ArrayExpress http://www.ebi.ac.uk/microarray‐as/aer/?#ae‐main[0]

Bioconductor http://www.bioconductor.org/

BioMoby http://biomoby.org/

BRB ArrayTools http://linus.nci.nih.gov/pilot/index.htm

caBio http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview/caBIO

CIBEX http://cibex.nig.ac.jp/index.jsp

DAVID http://david.abcc.ncifcrf.gov/

Developmental Therapy Program (DTP) NCI/NIH http://dtp.nci.nih.gov

Ensembl http://www.ensembl.org/index.html

European Bioinformatics Institute (EBI) http://www.ebi.ac.uk/

Gene Ontology Consortium http://www.geneontology.org/

GeneGo http://www.genego.com/

GenMAPP http://www.genmapp.org/

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

GoMiner http://discover.nci.nih.gov/gominer/

HAPI http://132.239.155.52/HAPI/

iHOP http://www.ihop‐net.org/UniPub/iHOP/

Inforsense http://www.inforsense.com/

Ingenuity http://www.ingenuity.com/

Inxight http://www.inxight.com/

Kyoto Encyclopedia of Genes and Genomes (KEGG) http://www.genome.ad.jp/kegg/

limmaGUI http://bioinf.wehi.edu.au/limmaGUI/

Mouse Genome Informatics (MGI) http://www.informatics.jax.org/

MIAME http://www.mged.org/Workgroups/MIAME/miame.html

Microarray Gene Expression Data Group (MGED Group) http://www.mged.org/

myGrid http://www.mygrid.org.uk/?&MMN_position=1:1

National Center for Biotechnology Information (NCBI) http://www.ncbi.nlm.nih.gov/

OMIM http://www.ncbi.nlm.nih.gov/sites/entrez?db=OMIM

OmniViz http://www.biowisdom.com/

Partek http://www.partek.com/

PubGene http://www.pubgene.uio.no/

R project http://www.r‐project.org/

Reactome http://www.genomeknowledge.org/cgi‐bin/frontpage?DB=gk_current

Seahawk applet http://biomoby.open‐bio.org/CVS_CONTENT/moby‐live/Java/docs/Seahawk.html

Spotfire http://www.spotfire.com/

Taverna project http://taverna.sourceforge.net/

The Institute for Genomic Research (TIGR) http://www.tigr.org/

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How to Cite close
Stubbs, Andrew P, Van Yper, Stefan JL, and van der Spek, Peter J(Jul 2008) Microarray Bioinformatics. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0005957.pub2]