Presentation on theme: "Basic Genomic Characteristic AIM: to collect as much general information as possible about your gene: Nucleotide sequence Databases ○ NCBI GenBank ○"— Presentation transcript:
Basic Genomic Characteristic AIM: to collect as much general information as possible about your gene: Nucleotide sequence Databases ○ NCBI GenBank ○ EMBL Nucleotide Sequence Database ○ DDBJ For Protein sequences ○ UniProtKB NCBI Reference Sequence (RefSeq)
Nucleotide sequence DB The 3 databases form an international collaboration. Each of the three groups collects a portion of the total sequence data reported worldwide, and all new and updated database entries are exchanged between the groups on a daily basis. You do not need to check all of them!
NCBI OMIM database Nucleotide databases and Genome Browser provide information on the gene nucleotide sequence (exon, intron, alternative splicing sites…) but give you very few information on gene function OMIM database provide a summary of all the literature concerning a gene.
Protein Databases Protein databases provide useful information about the function of gene: e.g. conserved protein domains,… UniProt is the reference database Interpro offer automatic protein annotation based on conserved domains RefSeq
Similarity search If your gene has no protein information Protein sequence available BLASTP against a non redundant protein database Protein sequence unavailable BLASTX against a non redundant protein database
Protein 3D structure Many proteins have the 3D structure determined. Biggest databases are: PDB NCBI Structure Group Dali They offer tools for the visualization
PDB database The visualization tools allows you to see the structure and the ligands (if presents), rotate the image and zoom-in
3D structure prediction Structure still available for a limited number of proteins Effort to predict protein structures based on sequences similarities Still not very accurate! SwissModel PSIPRED PredictProtein
Protein interaction databases AIM: find proteins that interact with your target IntAct: EBI resource to find interctors BioGRID: is a freely available interaction database from model organisms and humans.
Regulatory and metabolic pathways the classic “KEGG”:KEGG
miRNA specific resources Databases: miRNAMap: it present several useful information such as secondary structure, tissue specific expression and predicted target gene HMDD: is specific for disease-miRNA association MiRbase: is a searchable database of published miRNA sequences and annotation. Target Prediction tools: miRecords: is a good repository that shows confirmed target genes and predictions from several other software
C. Elegans specific tools WormBase: is the main resource of information on C. elegans. Expression pattern databaseHope lab Expression Pattern Database The Nematode Expression Pattern DataBase Caenorhabditis elegans Genetics and Genomics: provides links to many useful resources for C. elegans
Expression databases Allows exploratory analyses of multiple experiments Experiments need to be linked Require much information about how experiments where conducted = sources of variation Very different to genomic databases MIAME standard
GEO and ArrayExpress Databases provide: The raw data for each hybridization (e.g., CEL or GPR files) The final processed (normalized) data for the set of hybridizations in the experiment (study) (e.g., the gene expression data matrix used to draw the conclusions from the study) The essential sample annotation including experimental factors and their values (e.g., compound and dose in a dose response experiment) The experimental design including sample data relationships (e.g., which raw data file relates to which sample, which hybridizations are technical, which are biological replicates) Sufficient annotation of the array (e.g., gene identifiers, genomic coordinates, probe oligonucleotide sequences or reference commercial array catalog number) The essential laboratory and data processing protocols (e.g., what normalization method has been used to obtain the final processed data)
Problems: Difficult compare experiments Significant genes not highlighted Poor results visualization ArrayExpress is trying with its Atlas to solve this problems
Genevestigator It is JAVA visualization tool that summarizes results from thousands of high quality transcriptomic experiments Much easier to compare samples Open access to only some of the data and 1 probeset/gene