basic genomic characteristic aim: to collect as much general information as possible about your...
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INTRODUCTION TO BIOLOGICAL DATABASES
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!
Nucleotide sequence DB
Nucleotide sequence DB
Nucleotide sequence DB
Nucleotide sequence DB
Nucleotide sequence DB
NCBI Entrez
Present all the information available at NCBI for a gene. Entrez is a integrated searching tool across all the databases
Genome Browsers
NCBI Sequence Viewer
UCSC Genome Browser
ENSEMBL
NCBI Sequence Viewer
This is an example view of the human beta globin region on chr11
UCSC Genome Browser
ENSEMBL
ENSEMBL – genome view
ENSEMBL – Gene tree
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.
NCBI OMIM database
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
Protein databases - UniProt
Protein databases - UniProt
Protein databases - UniProt
Protein databases - UniProt
Similarity search
If your gene has no protein information
Protein sequence availableBLASTP against a non redundant protein
database
Protein sequence unavailableBLASTX against a non redundant protein
database
Protein 3D structure
Many proteins have the 3D structure determined. Biggest databases are:PDBNCBI Structure GroupDali
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
Swiss-Model
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.
IntAct
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 associationMiRbase: 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
MIAME
Experimental design Microarray design Extraction, preparation and labelling Hybridisation conditions Measurements: images, quantifications,
parameters Systematic error adjustments and
transformations
MIAME
Gene Expression Omnibus NCBI administered ~280,000 samples >100 organisms >1,000,000,000
measurements
Gene Expression Omnibus
Gene Expression Omnibus
Gene Expression Omnibus
Gene Expression Omnibus
Gene Expression Omnibus
ArrayExpress
EBI administered >7000 experiments Provide p-values Bioconductor
package
ArrayExpress
ArrayExpress
ArrayExpress
ArrayExpress
ArrayExpress
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
Genevestigator
ONCOMINE