Other biological databases
Biological systems
Sequence data
Protein folding and 3D structure
Taxonomic data
Literature
Pathways and networks
Protein families and domains
Small molecules
Whole genome data
Ontologies -GO
Biological systems
Other Biological Databases
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Transcription factor binding sites -TRANSFAC
Protein structure databases- PDB, SCOP, CATH
Protein family databases- Pfam, Prints, PROSITE etc.
Chemicals and small molecules -ChEBI
Gene expression databases –GEO, ArrayExpress
Metabolic pathways - Reactome, KEGG
Genome Databases- Ensembl, FlyBase, WormBase etc.
Human genetics-related databases –HapMap, dbSNP
Transcription factor binding sites
• TRANSFAC –database of eukaryotic transcription
factors: http://www.generegulation.com/pub/databases.html#transfac
• TESS –Transcription Element Search System –for
predicting transcription factor binding sites, uses
TRANSFAC: http://www.cbi.upenn.edu/tess
• TFsearch –for searching transcription factor binding
sites:
http://www.cbrc.jp/research/db/TFSEARCH.html
Protein structure databases
• Main resource is Protein Data Bank (PDB):
http://www.rcsb.org/pdb/
• Contains the spatial coordinates of macromolecule
atoms whose 3D structure has been obtained by
X-ray or NMR studies
• Proteins represent more than 90% of available
structures (others are DNA, RNA, sugars, viruses,
protein/DNA complexes…)
• Can search by PDB code
Searching MSD
http://www.ebi.ac.uk/msd -Search by PDB code
Protein structure-related databases
• Structural family databases based on PDB –
SCOP (http://scop.mrc-lmb.cam.ac.uk/scop/)
and CATH
(http://www.biochem.ucl.ac.uk/bsm/cath/)
• Predicted structures in SWISS-MODEL
(http://swissmodel.expasy.org//SWISSMODEL.html)
Protein family databases
• Databases that produce signatures for identifying
protein families or domains
• Used for functional classification of proteins
• E.g. Pfam, PROSITE, Prints, SMART,
TIGRFAMs etc.
• Integrated into single resource InterPro
(http://www.ebi.ac.uk/interpro)
InterProScan sequence search
Stand-alone
version available
InterPro text search
Search
keyword,
protein acc
or InterPro
acc
Results
for
protein
acc
Example
InterPro
entry
Chemicals and small molecules
• Chemical abstracts- http://www.cas.org/
• ChEBI- http://www.ebi.ac.uk/chebi
• KEGG –part of it includes chemicals
http://www.genome.jp/kegg
• ChemID plus -chemicals cited in NLM databases
http://chem2.sis.nlm.nih.gov/chemidplus/chemi
dlite.jsp
• MSD-Chem –ligands and chemicals in MSD
CheBI example entry
Hierarchy
for
chemicals
Gene expression databases
• NCBI Gene Expression Omnibus (GEO)
http://www.ncbi.nlm.nih.gov/geo/
• ArrayExpress http://www.ncbi.nlm.nih.gov/geo/
• Stanford microarray database http://genomewww5.stanford.edu/
• Can usually search for experiments or particular
expression profiles
GEO
search
page
Profiles search results
Specific
entry and
experiment
info
ArrayExpress
search results
What does the data look like?
• Info on experiment, array used, etc.
• Raw or processed tab delimited file containing
spots and their intensities cy3/cy5 ratios) across
different samples
• Files with meta data e.g. sample info, annotation
and coordinates of each spot on array
Proteomics: SWISS-2DPAGE
Enzymes and metabolic pathways
• Contain information describing enzymes,
biochemical reactions and metabolic pathways;
• ENZYME and BRENDA: nomenclature databases
that store information on enzyme names and
reactions;
• IntEnz: Integrated relational Enzyme database
Enzyme nomenclature
• E.C. (Enzyme Commission) numbers assigned based
on reactions they catalyze
• Hierarchy, high level groups:
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EC 1 –Oxidoreductases
EC 2 –Transferases
EC 3 –Hydrolases
EC 4 –Lyases
EC 5 –Isomerases
EC 6 –Ligases
EC example
Metabolic Pathway databases
• PATHGUIDE >200 pathways
• KEGG (Kyoto encyclopedia of genes and genomes):
http://www.genome.jp/kegg -includes:
– Database of chemicals, genes and networks (metabolic,
regulatory etc.)
– Well-curated and quite specific
• EcoCyc (Encyclopedia of E. coli K12 genes and
metabolism): http://ecocyc.org –curation of entries
genome
• Reactome –curated biological pathways:
http://www.reactome.org/
• GenMAPP –pathways contributed by users
http://www.genome.ad.jp/kegg
Different pathway in
different species: ->
comparison
Pathway in Reactome
Example of a pathway in BioCyc
Protein-protein interaction databases
• Protein-protein interaction databases store pairwise
interactions or complexes
• Can get 1 to more than 20,000 interactions per publication
• IntAct http://www.ebi.ac.uk/intact
• DIP (Database of Interacting Proteins) http://dip.doembi.ucla.edu/
• BIND (Biomolecular Interaction Network Database)
http://submit.bind.ca:8080/bind/
Protein-protein interactions in IntAct
Integrated functional interactions in STRING
Genome browsers
• Integrate sequence & functional data for a genome
• Ensembl –genome browser for major eukaryotic genomes,
e.g. human, mouse etc. http://www.ensembl.org
• UCSC browser -http://genome.ucsc.edu/
• FlyBase –Drosophila genome database:
http://www.ebi.ac.uk/flybase
• WormBase –C. elegans: http://www.wormbase.org
• PlasmoDB –Plasmodium (malaria): http://plasmodb.org
• Etc.
Ensembl genome browser
Ensembl gene view 1
Ensembl
gene view 2
Gene within context on chromosome
Human genetics databases
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GeneCards (http://www.genecards.org/)
HapMap (http://hapmap.ncbi.nlm.nih.gov/)
OMIM http://www.ncbi.nlm.nih.gov/omim
HGDP Human Genome Diversity Project
(http://hagsc.org/hgdp/files.html)
Mutation/polymorphism databases
Most of the databases are disease or gene
centric i.e. p53
dbSNP
http://www.ncbi.nlm.nih.gov/SNP/
Repository of all known mutation
(human and other organisms)
Where to find the databases
• Table of addresses for major databases and tools
• Nucleic Acids Research Database issue January
each year
• Nucleic Acids Research Software issue –new
• Expasy list of tools:
http://ca.expasy.org/links.html
Large scale data retrieval
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Programmatic access to many databases
MySQL access to some
BioMart access –public and private
FTP sites –large data downloads
Other tutorials
• http://www.ensembl.org/info/website/tutorials/ind
ex.html
• http://www.ebi.ac.uk/training/online/
• http://www.ebi.ac.uk/2can/home.html