GeneLists 2010课件.ppt

Accessing GO: QuickGO http://www.ebi.ac.uk/ego/ Other Ontologies http://www.ebi.ac.uk/ontology-lookup Gene Attributes Function annotation Biological process, molecular function, cell location Chromosome position Disease association DNA properties TF binding sites, gene structure (intron/exon), SNPs Transcript properties Splicing, 3’ UTR, microRNA binding sites Protein properties Domains, secondary and tertiary structure, PTM sites Interactions with other genes Sources of Gene Attributes Ensembl BioMart (eukaryotes) Entrez Gene (general) /sites/entrez?db=gene Model organism databases E.g. SGD: / Many others: discuss during lab Ensembl BioMart Convenient access to gene list annotation Select genome Select attributes to download Select filters What Have We Learned? Many gene attributes in databases Gene Ontology (GO) provides gene function annotation GO is a classification system and dictionary for biological concepts Annotations are contributed by many groups More than one annotation term allowed per gene Some genomes are annotated more than others Annotation comes from manual and electronic sources GO can be simplified for certain uses (GO Slim) Many gene attributes available from Ensembl and Entrez Gene Gene Lists Overview Interpreting gene lists Gene function attributes Gene Ontology Ontology Structure Annotation BioMart + other sources Gene identifiers and mapping Gene and Protein Identifiers Identifiers (IDs) are ideally unique, stable names or numbers that help track database records E.g. Social Insurance Number, Entrez Gene ID 41232 Gene and protein information stored in many databases ? Genes have many IDs Records for: Gene, DNA, RNA, Protein Important to recognize the correct record type E.g. Entrez Gene records don’t store sequence. They link to DNA regions, RNA transcripts and proteins e.g. in RefSeq, which stores sequence. NCBI Database Links /Database/datamodel/data_nodes.swf NCBI: U.S. National Center for Biotechnology Information Part of National Libr