Chapter Six Hyperlinks: Integrative Genomics—Hyperlinks
- HMDB - Human Metabolome Database (page 331):
http://www.hmdb.ca
- Visualization of metabolic pathways (page 331):
http://biochem.boehringer-mannheim.com/prodinfo_fst.htm?/techserv/metmap.htm
(Note: This link is no longer active; see ExPASy, Biochemical Pathways - Metabolic Pathways
http://www.expasy.ch/cgi-bin/show_thumbnails.pl)
- Allen, Allen Brain Atlas of anatomical gene expression in the brain (page 332):
http://www.brain-map.org
- BRENDA, Comprehensive enzyme information system (page 332):
http://www.brenda-enzymes.info
- DBD, Transcription factor prediction database (page 332):
http://www.transcriptionfactor.org
- EcoCyc, Encyclopedia of E. coli genes and metabolism (page 332):
http://ecocyc.org
- EPD, Eukaryotic Promoter Database (page 332):
http://www.epd.isb-sib.ch
- ExPASy, Thumbnail sketches of metabolism and cellular biochemistry (page 332):
http://www.expasy.ch/cgi-bin/search-biochem-index
- GNRF, Gene Expression Atlas of the Genomics Institute of Novartis Research Foundation (page 332):
http://symatlas.gnf.org/SymAtlas
- GOLD, Genomes Online Database (page 332):
http://www.genomesonline.org
- JASPAR, Transcription factor binding profile database (page 332):
http://jaspar.genereg.net
- KEGG, Kyoto Encyclopedia of Genes and Genomes (page 332):
http://www.genome.ad.jp/kegg/kegg2.html
- LIGAND, Database for enzymes, compounds, and reactions (page 332):
http://www.genome.ad.jp/dbget/ligand.html
- MetaCyc, Encyclopedia of metabolic pathways (HumanCyc is specialized for humans) (page 332):
http://metacyc.org and http://humancyc.org
- MIRAGE, Molecular Informatics Resource for the Analysis of Gene Expression (page 332):
http://www.ifti.org
- Protein Lounge, Databases of protein-protein interactions, pathways, transcription factors, etc. (page 332):
http://www.proteinlounge.com
(Note: As of Feb. 2, 2009, this domain was on Google's list of malicious sites, so we are not linking to it here. It is possible that the problem has now been corrected.)
- MIPS, Computational analysis of the Munich Information Center for Protein Sequences (page 332):
http://mips.gsf.de
- REACTOME, Curated pathway database with advanced query features (page 332):
http://www.reactome.org
- TRANSFAC, Transcription factor and gene regulatory database (page 332):
http://www.gene-regulation.com
- TRRD, Transcriptional Regulatory Regions Database (page 332):
http://www.bionet.nsc.ru/trrd
- UMDDB, University of Minnesota Biocatalysis/Biodegradation Database (page 332): http://umbbd.ahc.umn.edu/index.html (no longer active; see http://umbbd.msi.umn.edu)
- MIPS Mammalian Protein-Protein Interaction Database (page 333):
http://mips.gsf.de/proj/ppi
- MCA, Metabolic Control Analysis (page 333):
http://dbkgroup.org/mca_home.htm
- Gepasi 3, Biochemical kinetics simulation software (page 335):
http://www.gepasi.org
- Ingeneue, Gene network simulation software (page 338):
http://www.ingeneue.com
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