Links for Research on Inherited Retinal Diseases
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(Last updated January 1, 2002)
| BodyMap | |
|---|---|
| Osaka University, Japan | Data on tissue sources for ESTs (e.g., retina), many generated in Japan. Some of these data are available from other sources such as UniGene but not in this useful format. |
| http://cookie.imcb.osaka-u.ac.jp/bodymap/ | |
| CEPH / Généthon Integrated Physical Map | |
| Centre d'Etudes Polymorphisme Humain, Fondation Jean Dausset, Paris, France | Maps integrating linkage and physical data from CEPH/Généthon resources. The Whitehead Map includes most of these; use this site for details. |
| http://www.cephb.fr/bio/ceph-genethon-map.html | |
| CHLC – Cooperative Human Linkage Center | |
| Consortium of Univ. of Iowa, Harvard Med. School, Marshfield Med. Res. Foundation, Fox Chase Cancer Center | Framework linkage maps based on microsatellite markers (tri- and tetranucleotide repeats, many unique to this consortium) tested in CEPH families. The Whitehead Map includes some of these. |
| http://www.chlc.org/ | |
| EUROGEM | |
| European Gene Mapping Project, Imperial Cancer Research Fund, Hertsfordshire, UK | Framework linkage maps based on microsatellite markers (some unique to this consortium, others from Généthon), tested in CEPH families. The Whitehead Map includes some of these. |
| http://www.icnet.uk/axp/hgr/eurogem/HTML/eurogem.html | |
| GDB – Genome Data Base | |
| Johns Hopkins Univ. School of Medicine, Baltimore, Maryland | Central list of all cloned and/or mapped human DNA sequences, including genes, ESTs, microsatellites, etc. |
| http://gdbwww.gdb.org/ | |
| GenBank | |
| National Center for Biotechnology Information, NLB, NIH | Primary US database for all sequence data, including ESTs (in dbEST). |
| http://www.ncbi.nlm.nih.gov/Web/Genbank/ | |
| Généthon Linkage Map | |
| Généthon Human Genome Research Center | Linkage maps of Généthon-derived microsatellite markers (mostly dinucleotide) mapped in CEPH reference families. The Whitehead Map includes most of these; use this site for details. GENEXPRESS database at this site contains mapped ESTs, most in the Whitehead Map. |
| http://www.genethon.fr/genethon_en.html | |
| Human Gene Map | |
| National Center for Biotechnology Information, NLM, NIH | Integrated EST maps, best available at present but the Whitehead Map includes many of these. |
| http://www.ncbi.nlm.nih.gov/SCIENCE96/ | |
| Human Gene Mutation Database | |
| Institute of Medical Genetics, Cardiff, Wales | Tables of disease-causing mutations in humans. |
| http://www.cf.ac.uk/uwcm/mg/hgmd0.html | |
| LDB – Location Data Base | |
| Human Genetics Group, Dept. of Human Genetics, Princess Anne Hospital, Southampton, UK | Integrated genetic and physical maps of the human genome. The mapping algorithm is very effective but there will be errors in order and distances. |
| http://cedar.genetics.soton.ac.uk/public_html/ | |
| LENS (Linking ESTs and their associated Name Space) Database | |
| Computational Biology and Informatics, Univ. of Pennsylvania, Pittsburgh, PA | Database which links and resolves names of clones and ESTs from WashU, Merck and I.M.A.G.E. projects; most useful for identifying ESTs derived from a particular chromosome and tissue source. |
| http://agave.humgen.upen.edu/lens/ | |
| OMIM – Online Mendelian Inheritance in Man | |
| National Center for Biotechnology Information, NLM, NIH | Descriptions of all inherited human diseases, including symptoms, map location, causitive gene and mutations, if known. Usually up-to-date within 6 months; good search routines; new text is usuallyadded to the bottom of an entry so earlier text may be outdated. |
| http://www3.ncbi.nlm.nih.gov/Omim/ | |
| RetNet – Retinal Information Network | |
| The University of Texas Health Science Center, Houston | List of cloned and/or mapped genes causing inherited retinal degeneration and related tables. |
| http://www.sph.uth.tmc.edu/RetNet/ | |
| Stanford Radiation Hybrid Map | |
| Stanford Human Genome Center, Stanford University, Stanford, CA | STSs mapped on Stanford-generated radiation hybrids |
| http://shgc-www.stanford.edu/RHMap.html | |
| TIGR – The Institute for Genomic Research | |
| The Institute for Genomic Research, Rockville, MD | Proprietary and non-proprietary ESTs and sequence data from humans and other organisms. |
| http://www.tigr.org/tigr_info/tigr_info.html | |
| UniGene | |
| National Center for Biotechnology Information, NLM, NIH | Clusters of human ESTs, some mapped and some not. Can search on chromosome or tissue source, e.g., "retina", but may need to download each EST to find full summary information. Most are in the Human Gene Map. |
| http://www.ncbi.nlm.nih.gov/UniGene | |
| WashU-Merck Human EST Project | |
| Washington Univ., St. Louis, MO, and Merck and Co. | Major EST sequencing project; most data are available in GenBank etc.; use this site for EST details. Original DNA sequencing "traces" are available for veiwing. This may be helpful for identifying possible sequencing errors. |
| http://genome.wustl.edu/est/esthmpg.html | |
| Whitehead STS-Based Map | |
| Whitehead Institute for Biomedical Research, MIT Center for Genome Research, Boston, MA | Comprehensive maps integrating genetic, physical, STS, EST and radiation hybrid data. |
| http://www-genome.wi.mit.edu/cgi-bin/contig/phys_map | |
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| bionet.mutation mailing list | |
|---|---|
| BIOSCI | Discussion of all aspects of mutation research. This is a "prototype" newsgroup, which may eventually graduate to full newsgroup status. |
| Send subscription requests to biosci-server@net.bio.net | |
| HUM-MOLGEN mailing list | |
| Editors: Arthur A.B. Bergen, Carlo Gambacorti, Hans Goerl, Jurg Ott, Francis Ouelette, Robert Resta, Agnes Tay, Ed Wilcox, and Frank S. Zollmann | Comprehensive listserver (a public exchange of e-mail messages) for human molecular genetics, with several topics from which to choose. |
| http://www.informatik.uni-rostock.de/HUM-MOLGEN | |
| RD-List | |
| Dr. Jacqui Greenberg, Univ. of Capetown, SA | Listserver specializing in the molecular genetics of inherited retinal degeneration: gene mapping and cloning, mutation detection, etc. |
| Contact Dr. Greenberg at JG@anat.uct.ac.za | |
| RP-List | |
| Nicolas Graner, Liz Hare, St. Johns College, UK | Listserver for patients and others interested in retinitis pigmentosa and related diseases. |
| http://www.netspace.org/cgi-bin/lwgate/RPLIST/ | |
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|
There are too many news groups to cover adequately.
A few useful ones are: |
| bionet.genome.chromosomes
bionet.molbio.gdb bionet.molbio.genbank bionet.molbio.gene-linkage bionet.molbio.genome-program sci.med.vision |
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| AltaVista | |
|---|---|
| Digital Co. | Best overall Web search site. |
| http://www.altavista.digital.com/ | |
| Baylor Human Genome Sequencing Center | |
| Baylor College of Medicine, Houston, TX | Web site with several useful tools for molecular analysis, including a good "front-end" for BLAST searches. |
| http://gc.bcm.tmc.edu:8088/ | |
| Chromosome-specific Committees and Web sites | |
| GDB and HUGO sponsor Chromosome Editors for each human chromosome; the Editors are often involved in entering GDB data, conducting chromosome workshops, and maintaining chromosome databases. Names and contact information are available through the HUGO Web site. | |
| Chromosome-specific sequencing projects | |
| Several universities, consortia, and corporations have begun large-scale sequencing of human chromsome regions. These data are usually placed in central databases (e.g., GenBank) within a few weeks of sequencing, but raw data may be available earlier at the organizations' Web sites. AltaVista can find most of these sites. | |
| HUGO | |
| Human Genome Organisation, with regional offices in Bethesda, MD, London and Tokyo. | Voluntary, non-profit, international organization coordinating the Human Genome Project. |
| http://hugo.gdb.org/hugo.html | |
| NCBI | |
| National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD | Primary site for many government-sponsored genome databases. |
| http://www.ncbi.nlm.nih.gov/ | |
| Pedro's BioMolecular Research Tools | |
| Iowa State University | Very eclectic collection of Web sites, listed by category and rated for usefulness, which provides a jumping-off point for many unexpected resources. |
| http://www.public.iastate.edu/~pedro/research_tools.html | |
| SANBI – South African National Bioinformatics Institute | |
| The University of the Western Cape, Bellville, South Africa | Site for retinitis pigmentosa tissue-specific EST database development. |
| http://www.sanbi.ac.za/ | |
| SavvySearch | |
| Colorado State University | Experimental search site which sends a query to several sites simultaneously. |
| http://guaraldi.cs.colostate.edu:2000/ | |
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Supported by The Foundation Fighting Blindness, The George Gund Foundation, and the Hermann Eye Fund.
©1996-2008, Stephen P. Daiger, PhD and The University of Texas Health Science Center, Houston, Texas