Andrew P Stubbs, Erasmus University Medical Center, Rotterdam, The Netherlands
Stefan JL Van Yper, Erasmus University Medical Center, Rotterdam, The Netherlands
Peter J van der Spek, Erasmus University Medical Center, Rotterdam, The Netherlands
Published online: July 2008
DOI: 10.1002/9780470015902.a0005957.pub2
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
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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.
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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 | |
| ePath Affymetrix http://www.affymetrix.com/index.affx | |
| ePath ArrayExpress http://www.ebi.ac.uk/microarray-as/aer/?#ae-main[0] | |
| ePath Bioconductor http://www.bioconductor.org/ | |
| ePath BioMoby http://biomoby.org/ | |
| ePath BRB ArrayTools http://linus.nci.nih.gov/pilot/index.htm | |
| ePath caBio http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview/caBIO | |
| ePath CIBEX http://cibex.nig.ac.jp/index.jsp | |
| ePath DAVID http://david.abcc.ncifcrf.gov/ | |
| ePath Developmental Therapy Program (DTP) NCI/NIH http://dtp.nci.nih.gov | |
| ePath Ensembl http://www.ensembl.org/index.html | |
| ePath European Bioinformatics Institute (EBI) http://www.ebi.ac.uk/ | |
| ePath Gene Ontology Consortium http://www.geneontology.org/ | |
| ePath GeneGo http://www.genego.com/ | |
| ePath GenMAPP http://www.genmapp.org/ | |
| ePath GEO http://www.ncbi.nlm.nih.gov/geo/ | |
| ePath GoMiner http://discover.nci.nih.gov/gominer/ | |
| ePath HAPI http://132.239.155.52/HAPI/ | |
| ePath iHOP http://www.ihop-net.org/UniPub/iHOP/ | |
| ePath Inforsense http://www.inforsense.com/ | |
| ePath Ingenuity http://www.ingenuity.com/ | |
| ePath Inxight http://www.inxight.com/ | |
| ePath Kyoto Encyclopedia of Genes and Genomes (KEGG) http://www.genome.ad.jp/kegg/ | |
| ePath limmaGUI http://bioinf.wehi.edu.au/limmaGUI/ | |
| ePath Mouse Genome Informatics (MGI) http://www.informatics.jax.org/ | |
| ePath MIAME http://www.mged.org/Workgroups/MIAME/miame.html | |
| ePath Microarray Gene Expression Data Group (MGED Group) http://www.mged.org/ | |
| ePath myGrid http://www.mygrid.org.uk/?&MMN_position=1:1 | |
| ePath National Center for Biotechnology Information (NCBI) http://www.ncbi.nlm.nih.gov/ | |
| ePath OMIM http://www.ncbi.nlm.nih.gov/sites/entrez?db=OMIM | |
| ePath OmniViz http://www.biowisdom.com/ | |
| ePath Partek http://www.partek.com/ | |
| ePath PubGene http://www.pubgene.uio.no/ | |
| ePath R project http://www.r-project.org/ | |
| ePath Reactome http://www.genomeknowledge.org/cgi-bin/frontpage?DB=gk_current | |
| ePath Seahawk applet http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Seahawk.html | |
| ePath Spotfire http://www.spotfire.com/ | |
| ePath Taverna project http://taverna.sourceforge.net/ | |
| ePath The Institute for Genomic Research (TIGR) http://www.tigr.org/ | |
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