Databases and Web Sites for Neurogenetics

Thomas Brody1, Ward Odenwald1

1 National Institute of Neurological Disorders and Stroke, NIH, Bethesda
Publication Name:  Current Protocols in Neuroscience
Unit Number:  Appendix 5B
DOI:  10.1002/0471142301.nsa05bs28
Online Posting Date:  September, 2004
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library

Abstract

The goal of neurogenetics is an understanding of the genetic basis of brain structure and function. Neurogenetics deals with multiple areas of investigation, including the genetic basis of neural induction, patterning, cell fate specification, neuron maturation, axonal and dendritic organization, synapse function, and learning and behavior. This appendix provides links to databases and other Web sites used by neurobiologists for recovery of information about genes involved in neural development and neuron function. Special care has been taken to curate sites involving model organisms, since neurogenetics relies heavily on comparative genomics to establish gene function.

Keywords: neurogenetics; Web sites; neurobiology; model organism

     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Table of Contents

  • General Sites
     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Materials

GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Figures

Videos

Literature Cited

   http://www3.ncbi.nlm.nih.gov/entrez/query.fcgi
  PubMed/Medline Query, National Library of Medicine. As of 2004, this resource includes over 14 million citations for biomedical articles back to the 1950s.
   http://srs.ebi.ac.uk/srsbin/cgi‐bin/wgetz?‐page+srsq2+‐noSession
  SRS, European Bioinformatics Institute. A powerful data‐integration platform providing rapid access to life science data stored in more than 400 databases. Use this resource to recover almost any information, including structure, evolution, and literature, about any gene or protein of interest.
   http://www.neuroguide.com/neuroresac_4.html
  Neurosciences on the Internet. A compendium of databases related to all aspects of neurosciences.
   http://web.sfn.org/
  Society for Neuroscience. A nonprofit membership organization of basic scientists and physicians who study the brain and nervous system.
   http://sdb.bio.purdue.edu/fly/aimain/1aahome.htm
  The Interactive Fly, Purdue University. An encyclopedia of Drosophila genes and their homologs describing the conservation of gene function throughout animal evolution (also see below).
   http://www.aalas.org/
  American Association for Laboratory Animal Science. The “Links” page consists of the following subcategories: associations, comparative medicine departments, diagnostic labs, and testing alternatives. See, for example, University of California Center for Animal Alternatives and The Animal Welfare Information Center of U.S. Department of Agriculture.
   http://braininfo.rprc.washington.edu/
  BrainInfo. A database that helps identify and provide information relating to thousands of neuro‐anatomical terms.
Multiple Resource Sites
   http://www.ncbi.nlm.nih.gov/Database/index.html
  Database resources of NCBI. Major databases include: PubMed, nucleotide and protein sequences, protein structures, complete genomes, and taxonomy.
   http://us.expasy.org/
  ExPASy Molecular Biology Server, proteomics server of the Swiss Institute of Bioinformatics. Databases include Swiss‐Prot and TrEMBL, PROSITE, SWISS‐2DPAGE, and SWISS‐3DIMAGE.
   http://www.sanger.ac.uk/DataSearch/databases.shtml
  Database Resources of the Sanger Institute. Database resources include: (1) Pfam, a protein families database; (2) Rfam, an RNA families database of alignments; (3) Wormbase, a C. elegans genome database browser; and (4) SRS, a sequence retrieval system.
   http://www.ensembl.org/
  Ensembl Genome Browser, Sanger Center. BLAST server and sequence retrieval for several species, including human, chimp, mouse, rat, zebrafish, fugu, mosquito, fruitfly, C. elegans, and C. briggsae.
   http://restools.sdsc.edu/
  CMS Molecular Biology Resource, San Diego Supercomputer Center at UCSD. A compendium of tools and resources for molecular biology.
Molecular Analysis Sites
   http://www.ncbi.nlm.nih.gov:80/LocusLink/
  LocusLink, National Library of Medicine. LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci. It presents information on official nomenclature, sequence accessions, phenotypes, and precomputed BLAST, and includes links to UniGene clusters with further links to the HomoloGene resource, which contains literature links.
   http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide
  Entrez Nucleotide and Entrez Protein, National Library of Medicine. Redundant databases of sequences providing citations and other relevant links.
   http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein
  SwissProt, Swiss Institute of Bioinformatics. A curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post‐translational modifications, and variants), a minimal level of redundancy, and high level of integration with other databases.
   http://us.expasy.org/sprot/sprot‐top.html
  iProClass, Georgetown University. An integrated resource that provides comprehensive family relationships and structural/functional features of proteins. Consists of nonredundant Protein Information Resource (PIR; http://pir.georgetown.edu/home.shtml) and SwissProt/TrEMBL (http://us.expasy.org/sprot/) proteins organized with more than 36,290 PIR superfamilies, 145,300 families, 7255 domains, 1300 motifs, 280 post‐translational modification sites, and links to over 50 biological databases.
   http://pir.georgetown.edu/iproclass/
  NCBI BLAST server. Tools for recovery of protein and nucleic acid alignments.
   http://www.ncbi.nlm.nih.gov/blast/index.shtml
  Pfam, a collection of protein domain families. Collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families.
   http://www.sanger.ac.uk/Software/Pfam/
Model Organisms
Human Neurobiology and Bioinformatics Sites
   http://genome.ucsc.edu/cgi‐bin/hgGateway
  UCSC Genome Bioinformatics, Genome Bioinformatics Group of U.C. Santa Cruz. Human Genome and Human Gene Family Browsers.
   http://www3.ncbi.nlm.nih.gov/omim/
  Online Mendelian Inheritance in Man, NCBI. Catalog of human genes and genetic disorders.
   http://bioinfo.weizmann.ac.il/cards/
  GeneCards, Weizmann Institute of Science. A database of human genes, their products and their involvement in diseases.
   http://harvester.embl.de/
  Harvester, EMBL Heidelberg. Harvester caches and cross‐links public bioinformatic databases and prediction servers to provide fast access to protein specific bioinformatic information. Contains information on human proteins only.
   http://www3.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM
  Links to two dozen human genetic disease databases: OMIM locus‐specific mutation database links, NCBI variation databases, and related sites. Complied by the Human Genome Variation Society.
   http://www.genomic.unimelb.edu.au/mdi/dblist/dblist.html
  Includes locus‐specific mutation databases, disease‐centered mutation databases, and central mutation, and SNP databases.
   http://life2.tau.ac.il/GeneDis/
  GeneDis, Tel Aviv University. Human Genetic Disease Database: describes mutations in a dozen human genetic diseases.
   http://www.nlm.nih.gov/medlineplus/brainandnervoussystem.html
  MEDLINEplus Health Information: Brain and Nervous System Topics, National Library of Medicine, NIH. Links to dozens of sites related to human neural diseases.
   http://molgen‐www.uia.ac.be/ADMutations/default.cfm
  The Alzheimer Disease Mutation Database, Human Genome Variation Society. All reported mutations related to Alzheimer Disease. Mutations can be retrieved based on the gene, phenotype and publication.
   http://www.mic.ki.se/Diseases/C10.html
  Links pertaining to Nervous System Diseases, Karolinska Institute Library. Links to dozens of sites related to nervous system diseases.
   http://www‐grap.fagmed.uit.no/GRAP/homepage.html
  GRAP Mutant Database, University of Tromso, Norway. A database of mutant alleles of G‐protein Coupled Receptors, Family A. Contains data on around 10500 mutants published in 1380 papers.
Antibody Reagents and Cell Line Sources
   http://www.atcc.org/SearchCatalogs/CellBiology.cfm
  American Type Culture Collection (ATCC), Cell Lines and Hybridomas. ATCC's Cell Biology Collection is the most comprehensive and diverse of its kind in the world, consisting of over 4000 cell lines from over 150 different species. It holds over 950 cancer cell lines (including 700 human cancer cell lines) and over 1200 hybridomas for production of monoclonal antibodies, as well as a variety of special collections.
   http://www.antibodyresource.com/onlinecomp.html
  Antibody Resource Page. A to Z of online companies that sell antibodies.
   http://www.uiowa.edu/%7Edshbwww/
  Developmental Studies Hybridoma Bank at the University of Iowa. Under the auspices of the National Institute of Child Health and Human Development, the Developmental Studies Hybridoma Bank was established in 1986 to supply investigators with monoclonal antibodies useful for studies in developmental and cell biology.
Journals
   http://www.cell.com/
  Web site of Cell.
   http://www.bmn.com/
  BioMedNet; portal to Elsevier Life Science.
   http://dev.biologists.org/
  Web site of Development.
   http://link.springer.de/link/service/journals/00427/index.htm
  Web site of Development, Genes and Evolution.
   http://www.sciencedirect.com/science?_ob=JournalURL&_cdi=6766&_auth=y&_acct=C000000150&_version=1&_urlVersion=0&_userid=10843&md5=ef085ec524896b149001b6cdd6c09434
  Index of Developmental Biology.
   http://journals.wiley.com/1058‐8388/
  Web page for Developmental Dynamics.
   http://emboj.oupjournals.org/
  Web page for EMBO Journal.
   http://www.blackwellpublishing.com/journal.asp?ref=0953‐816X&site=1
  Web site for European Journal of Neuroscience.
   http://www.genesdev.org/
  Web site for Genes & Development.
   http://www.genetics.org/
  Web site for the journal Genetics.
   http://www.jcb.org/
  Web site for Journal of Cell Biology.
   http://jcs.biologists.org/
  Web site for Journal of Cell Science.
   http://www.jbc.org/
  Web site for Journal of Biological Chemistry.
   http://www.tandf.co.uk/journals/titles/01677063.html
  Web page for Journal of Neurogenetics.
   http://www.jneurosci.org/
  Web site for Journal of Neuroscience.
   http://www.elsevier.com/wps/find/journaldescription.cws_home/506090/description#description
  Web page for Mechanisms of Development.
   http://www.molbiolcell.org/
  Web site for Molecular Biology of the Cell.
   http://mcb.asm.org/
  Web site for Molecular and Cellular Biology.
   http://www.nature.com/
  Web site for the Nature journals.
   http://www.nature.com/ng/
  Web page for Nature Genetics.
   http://www.nature.com/neuro/
  Web page for Nature Neuroscience.
   http://www.nature.com/nrg/
  Web page for Nature Reviews Genetics.
   http://www.nature.com/nrn/
  Web page for Nature Reviews Neurogenetics.
   http://www.neuron.org/
  Web site for the journal Neuron.
   http://www.pnas.org/
  Web site for Proceedings of the National Academy of Sciences U.S.A.
   http://www.sciencemag.org/
  Web site for the journal Science.
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library