Human Genome Databases Menu

OMIM (Online Mendelian Inheritance in Man)
This database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and colleagues at NCBI, Bethesda, Maryland.

GDB (Genome DataBase)
GDB holds data on Human gene loci, polymorphisms, mutations, probes, genetic maps, GenBank, citations and contacts.

Human Genome Map Search (Pennsylvania University)
Human Genome Map Search retrieves GenBank entries that have been mapped to positions on human chromosomes and finds all the non-human homologs of those entries. The query uses map data from the Genome DataBase.

Human Chromosome-specific databases

Human genetic chromosomal maps (CPROP)
Human genetic chromosomal PostScript maps have been produced automatically from the GDB data.

Human Chromosome Ideograms (Washington University)
can be selected and displayed, courtesy of David Adler.

6ace (ACEDB-style human chromosome 6 data)
This is the ACeDB-style database of human chromosome 6 from the Sanger Centre.

11db (ACEDB-style human chromosome 11 data)
This is the ACeDB-style database of human chromosome 11 from Peter Little's group at Imperial College.

22ace (ACEDB-style human chromosome 22 data)
This is the ACeDB-style database of human chromosome 22 from the Sanger Centre.

Genome Navigator: Whitehead/MIT STS-based Map of the Human Genome
Genome Navigator is an attempt to provide a visual interactive gateway to major databases containing physical and genetic mapping information about the human genome.

Genomic maps of these organisms are displayed using DerBrowser, a Java applet, designed as a universal tool to display and navigate various types of maps. Among other features, it allows a user to query external databases about any map object.

GeneCards - integrated biomedical genetic information
Although it will take some years until the human genome is totally sequenced, and still a much longer time to learn about the functions of the products of those genes, the complex organization and the vast amount of biomedical information already accessible often cause certain problems that are somehow connected to the phenomenon of "information overflow" and the often very time-consuming process of information retrieval or mining. Thus, many scientists feel that new approaches to organize scientific information are urgently needed.

GeneCards is a database that intends to address some of these problems by integrating biomedical information taken from several sources (GDB, MGD, OMIM, SWISS-PROT, HGMD, Doctor's Guide to the Internet), and by presenting them in a way facilitating a quick.

Whitehead/MIT STS-Based Map of the Human Genome
This contains YAC screening data for several thousand STSs. For each STS, information is held on the following types of raw data (where available):

Chromosomal assignments
YAC library screening results
Radiation hybrid panel screening results

In addition, information is available on the following preliminary preliminary analyses:

Doubly-linked YAC contigs
Singly-linked YAC contigs
Radiation hybrid maps
Integrations between genetic, radiation hybrid, and YAC contig maps.

Transcript Map of the Human Genome
A small portion of each cDNA sequence is all that is needed to develop unique gene markers, known as sequence tagged sites or STSs, which can be detected in chromosomal DNA by assays based on the polymerase chain reaction (PCR). To construct a transcript map, cDNA sequences from a master catalog of human genes were distributed to mapping laboratories in North America, Europe, and Japan. These cDNAs were converted to STSs and their physical locations on chromosomes determined on one of two radiation hybrid (RH) panels or a yeast artificial chromosome (YAC) library containing human genomic DNA. This mapping data was integrated relative to the human genetic map and then cross-referenced to cytogenetic band maps of the chromosomes. (Further details are available in the accompanying article in the 25 October issue of SCIENCE).

The histograms reflect the distributions and densities of genes along the chromosomes. Because the individual genes (>16,000) are too numerous to represent, images have been chosen to illustrate the myriad aspects of human biology, pathology, and relationships with other organisms that can be revealed by analysis of genes and their protein products.

Human Telomere Information
This is a section of GenLink's Teldb giving literature citations and other information on human telomeric regions.

MHCDB
This is an ACeDB-style database holding the Human Major Histocompatibility Database. It is largely superceded by '6ace', above.

The Genetic Location Database (LDB)
Ldb is an analytical database for constructing fully integrated genetic and physical maps. The ldb program generates an integrated map (known as the summary map) from partial maps of physical, genetic, regional, somatic hybrid, mouse homology and cytogenetic data.

The summary maps and the data used to build up such maps are available from this site. The files for each chromosome are stored in the same directory which include the summary map, partial maps, lod files and the parameter files. As this server is experimental many of the chromosome directories are incomplete with the most complete map sets being chromosomes 1,9,21 and X.

The dysmorphic human and mouse homology database
This consists of three separate databases of human and mouse malformation syndromes together with a database of mouse/human syntenic regions. The mouse and human malformation databases are linked together through the chromosome synteny database. The purpose of the system is to allow retrieval of syndromes according to detailed phenotypic descriptions and to be able to carry out homology searches for the purpose of gene mapping. Thus the database can be used to search for human or mouse malformation syndromes in different ways:-

By specifying specific malformations or clinical features, or chromosome locations.
By Homology.
By asking for human syndromes located at a chromosome region syntenic with a specific mouse chromosome region (and vice versa from human to mouse).

BodyMap - Anatomical Expression Database of Human Genes
BodyMap is a data bank of expression information of human genes, novel or known, in various tissues or cell types. It is created by random sequencing of clones in 3'-directed cDNA libraries. Since these clones were not amplified, redundancy of the same sequence reflects the quantitative aspect of gene expression in various tissues.

You can enter your sequence and it will be matched using fasta to the cDNA sequences in this database.

CEPH-Genethon integrated map
This page allows you to search the CEPH-Genethon mapping data used to build the first generation physical map of the human genome. It gives information on the CEPH YAC library and the QUICKMAP database with the infoclone program to get information about a STS or a YAC.

CEPH Genotype database
The Centre d'Etude du Polymorphisme Humain (CEPH) maintains a database of genotypes for all genetic markers that have been tested in the reference families for linkage mapping of the human chromosomes.

browse data by chromosome, probe, D-number, Gene name and Heterozygote frequency
output data for several markers on the same chromosome in CEPH, LINKAGE and CRIMAP formats.
CEPH Collaborators can now submit data for new markers directly through Internet by using a browser supporting JAVA applets.

All genotypes contributed to the CEPH database are also available by anonymous FTP server. Genotypes, markers description, pairwise lodscores may be downloaded from the FTP server. In addition, the server contains databases for published CEPH consortium maps and also breakpoint maps.

Cooperative Human Linkage Center (CHLC)
The goal of the Cooperative Human Linkage Center is to develop statistically rigorous, high heterozygosity genetic maps of the human genome that are greatly enriched for the presence of easy-to-use PCR-formatted microsatellite markers.

Genetic maps showing the positions of genetic markers
- Integrated Maps showing the position of genetic markers constructed using genotype data from the CEPH reference panel.
- CHLC Marker Maps showing the positions of CHLC generated markers in various reference maps.
Search by name for information on markers.
- Search by name for information on markers, including map location primer and pcr conditions, and sequence templates.
- Likely locations of current CHLC markers, in Version 2.0 Skeletal Maps
- Tables of CHLC markers characterized by linkage analysis.
- List of full information on markers generated by CHLC
  - In Current Linkage Map
  - Candidate Linkage Markers
  - Somatic Cell Hybrid Assigned
- Prior versions of the CHLC generated markers.
- Marshfield CA-repeat Markers
  - Table of initial typing data
  - Table of sequence data
  - Table of PCR Primers
CHLC publications.
- Science Maps and Data
- Copies of the CHLC Newsletter
CHLC project information.

Radiation Hybrid Mapping data (RHdb)
Radiation hybrid maps are an indispensable alternative to genetic maps as they can include non-polymorphic markers and are also powerful enough to order unresolved genetic clusters of polymorphic STSs. An international collaborative project has been started which will produce a large number of these hybrids for the human genome. This in turn will allow the generation of a very precise STS map that will be indispensable in the study of multifactorial diseases.

RHdb, the radiation hybrid database is an archive of raw data with links to other related databases. The main data is stored in a relational database. Submissions to this database are made using a standard format. Various export formats will be supported, as well as different ways of accessing the data.

dbEST Expressed Sequence Tag Database
The dbEST Database holds many Human ESTs.

UniGene - Unique Human Gene Sequence Collection
This holds clusters of human EST sequences that represent the transcription products of distinct genes.

These sequences are being used for transcript mapping in collaboration with several genome mapping centers. Some of the clusters have already been localized to chromosomes, but more detailed mapping map information is not available at this time.

dbSTS Sequence Tagged Site Database
The dbSTS Database holds many Human STSs.

Whitehead Institute/MIT Genome Center

Human YAC screening data for sequence tagged sites (STSs) screened on the CEPH mega-YAC library with over 1100 contigs assembled using double linkage between STSs.
For each STS, they report addresses for the YACs found to contain the STS.
Human, Rat and Mouse marker map data files.

V BASE: A Directory of Human Immunoglobulin V Genes
A directory of human immunoglobulin germline variable region sequences compiled from over a thousand published sequences (including those in the current releases of the Genbank and EMBL data libraries). There are seven directories: D, JH, JK, JL, VH, VK and VL. Each directory consists of a folder or file containing the germline sequences and a file containing the corresponding reference list.

Human CpG Island database
Look at the Human CpG Island database. This is a flat file containing a description of genes and their associated CpG islands.

Human population genetics database (Genography)
The Genography project comprises four parts:

database (DNAbase)
- object-oriented database for population genetic data
- includes data from multiple species
- includes data from individuals as well as population samples
- includes cultural and linguistic data
- data entry, editing, and selection via hybrid SQL/OQL subset
analysis
- a graphical front-end for data selection and data analysis programs
- allows selection of subsets of data by area and marker
- carries out interpolation, principal components analysis, wombling, removal of principal components, and tree-building
- saves results and displays result datasets
- allows full control over parameters of analysis and display
simulation (Diaspora)
- cellular automaton simulation of thousands of generations of human genetic and cultural evolution
- diaspora is group movement: colonization, migration, and invasion
- density and technology affect birth, death, survival, and diaspora rates
- variable terrain with local carrying capacities
- carrying capacity affected by technological development
- genetic loci, with mutation and admixture dynamics
- linguistic characters, with shift and creolization dynamics
- cultural traits, with ogamy, diaspora, and technological development
monitor
- background monitoring and data-mining of Genography-database
- controls access to data according to authorization
- searches and logs errors and anomalies
- attempts to detect and report patterns

ANTHONY NOLAN RESEARCH INSTITUTE
The WHO Nomenclature and HLA Sequence alignments are availble from this site, together with monthly updates.

The Human Gene Mutation Database - HGMD (Cardiff)
This database represents a first attempt to collate the majority of known (published) gene lesions responsible for human inherited disease. Originally established for the study of mutational mechanisms in human genes (Cooper and Krawczak 1993), these databases have acquired a much broader utility in that they currently represent the only available comprehensive reference source to the spectrum of mutations underlying human genetic disease. They thus provide information of practical diagnostic importance to (i) researchers in human molecular genetics, (ii) physicians interested in a particular inherited condition in a given patient or family and (iii) genetic counsellors.

The Point Mutation Database
The Micro-Deletion Database
Links to Locus Specific Mutation Databases

Mutation Database Website
Information on nomenclature and design of mutation databases.

Documentation of the progress of the initiative.
Proposals from working groups.
Announcements
Publications in the area of Mutation Databases

PAH Genes and alleles (PAHDB)
Mutation data were collated from both published articles and personal communications of 80 investigators from the PAH Mutation Analysis Consortium in 26 countries.

Searchable fields of the database available to users are: mutation name, polymorphic haplotype, population, geographic location, gene region, codon number, mutation type, substitution, phenotype, and author's name.

Breast Cancer Mutation Data Base (BIC)
A resource for the molecular biologist investigating inherited breast cancer providing a central repository for information regarding breast cancer susceptibility genes mutations and polymorphisms.

This requires you to register as a BIC member.

Protein Mutation Database
PMD is based on literature (not on proteins); that is, each entry of the database corresponds to one article which describes protein mutations.

BTKbase - agammaglobulinemia XLA-causing mutations
BTKbase, mutation database for X-linked agammaglobulinemia XLA-causing mutations on the gene for Bruton's tyrosine kinase (BTK).

The database contains mutation and patient information for more than 350 patients. Submission to the database can be made with the submission form available in Web. This program also checks the information given and formats it suitable for addition into the database.

The detailed format of the database is available in a Feature Table Description. The database has been coded such that it is easy to read and suitable for computer programs. The database follows the conventions of sequence databases.

In addition to BTKbase, some other immunodeficiency mutation registries (IDbases) have been collected. They all follow the same guidelines, which including a Patient Identity Number (PIN), which identifies each patient in a unique and simple but still unambiguous way. Also the basis of PIN system is described on BTKbase homepages.

von Willebrand Factor (vWF) Database
Databases of point mutations, insertions, deletions, and polymorphisms found in von Willebrand Factor.

Mutations database
Polymorphisms in the vWF gene and pseudogene
Intron 40 polymorphism
References etc.

HAMSTeRS - Haemophilia A Mutation, Search, Test and Resource Site
Over the last decade there has been a dramatic increase in our understanding of the pathology of haemophilia A in molecular terms, at the levels both of nucleic acid sequence and to a much lesser extent, protein structure.

A Review of the Molecular Genetics of Haemophilia A
Submit a Mutation
Search Database
Bioinformatics of point mutations
Factor VIII Model Structure
Online Methods
Links to other sites

BIOMDB - Database of mutations causing tetrahydrobiopterin deficiencies
BIODEF is a locus-specific database with detailed records of disease-producing allelic variations and natural polymorphic markers.

MutRes - List of Mutation Resources
MutRes is a public list of databases, websites, programs and people related to collection and computational analysis of mutations.

MutRes relies on mutation database community for its accuracy of data. If you know unlisted resources or want to add to an existing entry, please use the MutRes Web submission form.

MutRes is made available through Thure Etzold's Sequence Retrieval System (SRS). It allows full text searching and instant hypertext linking to Web resources.

Human Genome Diversity Project FAQ
The Human Genome Diversity Project (the "HGD Project") is an international project that seeks to understand the diversity and unity of the entire human species. The HGD Project is still largely in its planning stages, seeking the best ways to reach its goals. We hope this document will provide important background information to help people gain a better understanding of this evolving initiative.

HGP Human Genome Project at Oak Ridge National Labs
This provides information on the organization and sequencing of the human genome.

Search HUM-MOLGEN mailing-list
The HUM-MOLGEN mailing-list service gives access to the archives of this mailing list for Biologists and Clinicians, allows posting of articles, information on all aspects of the human genome project, biotechnology, computational genetics, diagnostics, education, internet resources, literature and acts as a meeting place for bioscientists and clinicians.

As a part of HUM-MOLGEN Biotechnology you can find a Register of Biotechnology Companies (Name, Address, Phone, Fax, E-Mail, short description).

Human Genome Project Information
Information on the US DOE Genome project.

Human Genome Newsletter is available online and searchable via this service.
Calendar of Genome-Related Events
Ethical, Legal, and Social Issues

Guide to diagnostic services for genetic diseases (italian)

E-Mail: Support@hgmp.mrc.ac.uk