Download A.A. 2008-2009 CORSO DI BIOINFORMATICA per il CLT in

II LEZIONE
• Database di interesse per la genetica e la
biologia molecolare
• Portali per l'accesso a database e servizi
bioinformatici
DATABASES AND DATA RETRIEVAL
Biosequences and Gene-related info
DATABASE DI GENETICA E BIOLOGIA MOLECOLARE
OMIM
Online Mendelian Inheritance in Man
EntrezGene curated sequence and descriptive information
about genetic loci
GenCards
database of human genes, their products and their
involvement in diseases
HGMD
Human Gene Mutation Database: information
about disease-causing mutations in genes
dbSNP
the NCBI database of genetic variation (Single
Nucleotide Polymorphism)
DATABASE DI GENETICA E BIOLOGIA MOLECOLARE
OMIM
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM
EntrezGene
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=gene
GenCards
http://bioinformatics.weizmann.ac.il/cards/
HGMD
http://www.hgmd.cf.ac.uk/ac/index.php
dbSNP
http://www.ncbi.nlm.nih.gov/projects/SNP/
OMIM
Online Mendelian Inheritance in Man
Catalogo di geni umani e malattie genetiche (Dr. Victor A.
McKusick, Johns Hopkins + NCBI)
Contiene informazione testuale, riferimenti bibliografici e links
a MEDLINE, sequenze e ad altre risorse
OMIM gene map
Posizioni di mappa citogenetica di geni-malattia e altri geni
descritti in OMIM
OMIM morbid map
Posizioni di mappa citogenetica di geni-malattia indicizzati in
OMIM
Use OMIM
to explore
Rett
syndrome
There are entries
for both the
disease and the
gene
OMIM number
Link to NCBI map viewer
OMIM
Numbering and Symbols
ID e’ un numero di 6 cifre.
1----- (100000- ) Autosomal dominant (before 1994)
2----- (200000- ) Autosomal recessive (before 1994)
3----- (300000- ) X-linked loci or phenotypes
4----- (400000- ) Y-linked loci or phenotypes
5----- (500000- ) Mitochondrial loci or phenotypes
6----- (600000- ) Autosomal loci or phenotypes
Preceduto sa un simbolo:
* = gene of known sequence
# descriptive entry, a phenotype, not a locus
+ gene of known sequence and a phenotype.
% confirmed mendelian phenotype or phenotypic locus but molecular
basis is not known
No symbol phenotype for which the mendelian basis, although
suspected, has not been clearly established or that the separateness
of this phenotype from that in another entry is unclear
OMIM
Varianti alleliche
stesso ID piu’ un altro numero di 4 cifre.
Sono MUTAZIONI CHE CAUSANO MALATTIE
ENTREZ GENE
Interfaccia unificata per cercare
informazioni su sequenze e loci genetici. Presenta informazioni
sulla nomenclatura ufficiale, accession numbers, fenotipi, MIM
numbers, UniGene clusters, omologia, posizioni di mappa e link a
numerosi altri siti web.
ENTREZ GENE
ENTREZ GENE
ENTREZ GENE
GeneCards
Weizmann Institute of Science, Israele
GeneCards is a database of human genes, their products and
their involvement in diseases. It offers concise information about
the functions of all human genes that have an approved symbol,
as well as selected others.
The information presented here has been automatically
extracted from various resources. GeneCards™ is particulary
useful for people who wish to find information about genes of
interest in the context of functional genomics and proteomics.
http://www.genecards.org/
GeneCards
INFORMAZIONI SU
• Aliases and Additional Descriptions
• Chromosomal Location
• Proteins
• Protein Domains/Families/Ontologies
• Transcripts/Sequences
• Expression in Human Tissues
• Similar Genes in Other Organisms
• Related Human Genes - Paralogs
• SNPs/Variants
• Disorders & Mutations
• Medical News
• Research Articles
• Links to the entry of the gene in Other Genome Wide
Resources, in general or specialized databases
Gene Ontology
• Gene product function(s) definitions???
• Gene Ontology (GO) is a controlled
vocabulary that can be applied to all
organisms even as knowledge of gene and
protein roles in cells is accumulating and
changing.
• It is used to annotate genes.
• It is computable biological knowledge!
• Parent-child relationship and hierarchical
organization.
• EXAMPLE: Nebulin gene is associated to
different terms defining:
• biological process
• molecular function
• cellular component
GeneCards is an integrated database of human genes that
includes automatically-mined genomic, proteomic and
transcriptomic information, as well as orthologies, disease
relationships, SNPs, gene expression, gene function and more.
GeneNote is a database of human genes and their expression
profiles in healthy tissues (Weizmann Institute of Science
DNA array experiments, Affymetrix HG-U95 )
GeneAnnot provides a revised and improved annotation of
Affymetrix probe-sets from HG-U95, HG-U133 and HG-U133
Plus2.0.
GeneLoc presents an integrated map for each human
chromosome, based on data integrated by the GeneLoc
algorithm. GeneLoc includes further links to GeneCards,
NCBI's Human Genome Sequencing, UniGene, Genome
Database, and mapping resources.
GeneTide is an automated system for human transcripts
(mRNA & ESTs) annotation and elucidation of de-novo
genes.
HGMD
http://www.hgmd.cf.ac.uk/ac/index.php
• Human Gene Mutation Database (HGMD) raccoglie le
mutazioni conosciute (pubblicate) in geni umani, responsabili
di malattie genetiche
• Creato per studiare il meccanismo delle mutazioni nel
genoma umano, per riconoscere le regioni e i loci ipermutabili
• Ora e’ importante anche come raccolta di dati. Utile per
diagnosi molecolare di patologie e consulenza genetica.
• Non include mutazioni somatiche o mitocondriali, mutazioni
silenti.
• Dal marzo 1999, HGMD include disease-associated
polymorphisms.
• Basato sull’analisi di >250 riviste scientifiche.
HGMD
dbSNP
http://www.ncbi.nlm.nih.gov/SNP/
Gli SNPs (single
nucleotide
polymorphisms), sono
polimorfirsmi di singoli
nucleotidi, che si
ritrovano
approssimativamente
ogni 100-300 basi nel
genoma umano.
Sono molto utilizzati
come marcatori genetici
soprattutto in studi di
associazione.
dbSNP
http://www.ncbi.nlm.nih.gov/projects/SNP/
Portali per l'accesso a database e servizi
bioinformatici
NCBI (SNP,SAGE, Gene Expression Omnibus, Cancer
Chromosomes database, …)
ExPASy Proteomics Server (http://www.expasy.org/)
EBI (EMBL Nucleotide Database, UniProt Knowledgebase,
Macromol. Structure Database, ArrayExpress, Ensembl,…,
TOOLBOX) (http://www.ebi.ac.uk/services/)
RefSeq project description and update is online:
http://www.ncbi.nlm.nih.gov/books/NBK21091/