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II LEZIONE

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

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II LEZIONE

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  1. II LEZIONE • Database di interesse per la genetica e la biologia molecolare • Portali per l'accesso a database e servizi bioinformatici

  2. DATABASES AND DATA RETRIEVAL Biosequences and Gene-related info

  3. 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)

  4. 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/

  5. 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

  6. Use OMIM to explore Rett syndrome

  7. There are entries for both the disease and the gene

  8. OMIM number Link to NCBI map viewer

  9. 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

  10. OMIM Varianti alleliche stesso ID piu’ un altro numero di 4 cifre. Sono MUTAZIONI CHE CAUSANO MALATTIE

  11. 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.

  12. ENTREZ GENE

  13. ENTREZ GENE

  14. ENTREZ GENE

  15. 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/

  16. 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

  17. 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

  18. 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.

  19. 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, HGMDinclude disease-associated polymorphisms. • Basato sull’analisi di >250 riviste scientifiche.

  20. HGMD

  21. 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.

  22. dbSNP http://www.ncbi.nlm.nih.gov/projects/SNP/

  23. 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/)

  24. RefSeq project description and update is online: • http://www.ncbi.nlm.nih.gov/books/NBK21091/

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