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GENOME ANNOTATION AND
FUNCTIONAL GENOMICS
The protein sequence perspective
GENOME ANNOTATION
• Two main levels: – STRUCTURAL ANNOTATION – Finding genes
and other biologically relevant sites thus building up a model of genome as objects with specific locations
– FUNCTIONAL ANNOTATION – Objects are used in database searches (and expts) aim is attributing biologically relevant information to whole sequence and individual objects
WHY PROTEIN RATHER THAN DNA?
• Larger alphabet -more sensitive comparisons• Protein sequences lower signal to noise ratio• Less redundancy and no frameshifts• Each aa has different properties like size, charge etc• Closer to biological function• 3D structure of similar proteins may be known• Evolutionary relationships more evident• Availability of good, well annotated protein sequence
and pattern databases
Large-scale genome analysis projects
• Rate-limiting step is annotation
• Whole genome availability provides context information
• Main goal is to bridge gap between genotype and phenotype
Definitions of Annotation• Addition of as much reliable and up-to-date
information as possible to describe a sequence• Identification, structural description,
characterisation of putative protein products and other features in primary genomic sequence
• Information attached to genomic coordinates with start and end point, can occur at different levels
• Interpreting raw sequence data into useful biological information
ANNOTATION/FUNCTION CAN BE MAPPED TO DIFFERENT LEVELS:
ORGANISM -phenotypic function (morphology, physiology, behaviour, environemntal response), context NB
CELLULAR -metabolic pathway, signal cascades, cellular localisation. Context dependent
MOLECULAR -binding sites, catalytic activity, PTM, 3D structure
DOMAIN
SINGLE RESIDUE
Annotation is the description of:
• Function(s) of the protein• Post-translational modification(s) • Domains and sites • Secondary structure• Quaternary structure• Similarities to other proteins• Disease(s) associated with deficiencie(s) in the
protein• Sequence conflicts, variants, etc.
Additional information for proteins
• ALTERNATIVE PRODUCTS
• CATALYTIC ACTIVITY
• COFACTOR
• DEVELOPMENTAL STAGE
• DISEASE
• DOMAIN
• ENZYME REGULATION
• FUNCTION
• INDUCTION
• PATHWAY
• PHARMACEUTICALS
• POLYMORPHISM
• PTM
• SIMILARITY
• SUBCELLULAR LOCATION
• SUBUNIT
• TISSUE SPECIFICITY
Amino-acid sites are:• Post-translational modification of a residue• Covalent binding of a lipidic moiety• Disulfide bond• Thiolester bond• Thioether bond• Glycosylation site• Binding site for a metal ion• Binding site for any chemical group (co-enzyme, prosthetic
group, etc.)
Regions:
• SIGNAL SEQUENCE
• TRANSIT PEPTIDE
• PROPEPTIDE
• CHAIN
• PEPTIDE
• DOMAIN
• ACTIVE SITE
• DNA BIND SITE
• METAL BIND SITE
• MOLECULE BIND SITE
• TRANSMEMBRANE
Annotation sources:
• publications that report new sequence data• review articles to periodically update the
annotation of families or groups of proteins• external experts• protein sequence analysis
Approaches to functional annotation:
Automatic annotation (sequence homology, rules, transfer info from pdb)
Automatic classification (pattern databases, clustering, structure)
Automatic characterisation (functional databases) Context information (comparitive genome analysis, metabolic
pathway databases) Experimental results (2D gels, microarrays) Full manual annotation (SWISS-PROT style)
PROTEIN SEQUENCE ANALYSIS• Protein sequence can come from gene predictions,
literature or peptide sequencing• Analysis on different levels:
– molecular– cellular– organism
• Simplest case- match for whole sequence in database- determination of structure and function
• In between- partial matches across sequence to diverse or hypothetical proteins
• Difficult case- no match, have to derive information from amino acid properties, pattern searches etc
From sequence
to function
Predicting function from sequence similarity
• Orthologues- arose from speciation, same gene in different organisms -can have <30% homology
• Paralogues- from duplication within a genome, second copy may have new or changed function
(difficult to distinguish between otho- and paralogues unless whole genome is available)
• Equivalog- proteins with equivalent functions• Analog- proteins catalyzing same reaction but not
structurally related • Some enzymes may have seq similarity simply because
common catalytic site, substrate, pathway.
TYPES OF HOMOLOGY
PROTEIN/DOMAIN
A B
Duplication within species
Superfamily
Paralogues may have different
functions
Speciation
Orthologues may have different functions, if same -
EquivalogsB2B1
Sequence homology in genomes
When you do a whole genome BLAST search there is a general pattern of results:
Common genes
Maverick genes shared with some other species
Incorrect predictions
Maverick genes unique function
Maverick genes tend to diverge more frequently than core genes
Using homology information for automatic annotation- automatic
annotation of TrEMBL as an example
Requirements for automatic annotation
• Well-annotated reference database (eg SWISS-PROT)
• Highly reliable diagnostic protein family signature database with the means to assign proteins to groups (eg CDD, InterPro, IProClass)
• A RuleBase to store and manage the annotation rules, their sources and their usage
Direct Transfer
• Search target• Transfer annotation to
target database
• Example:FASTA against sequence database and transfer of DE line of best hit
TargetTarget
XDBXDB
Multiple Sources
• Usually more than one external database is used
• Combine the different results
TargetTarget
XDBXDB
Conflicts
• Contradiction
• Inconsistencies
• Synonyms
• Redundancy
Translation
• Use a translator to map XDB language to target language
TargetTarget
XDBXDB
Translation Examples• ENZYME TrEMBL CA L-ALANINE=D-ALANINECC -!- CATALYTIC ACTIVITY: L-ALANINE=CC D-ALANINE.
• PROSITE TrEMBL/SITE=3,heme_ironFT METAL IRON
• Pfam TrEMBL FT DOMAIN zf_C3HC4FT ZN_FING C3HC4-TYPE
Demands on a system for automated data analysis and
annotation• Correctness
• Scalability
• Updateable
• Low level of redundant information
• Completeness
• Standardized vocabulary
What do we have?
• SWISS-PROT• RuleBase• TrEMBL• PROSITE (and Pfam, PRINTS, ProDom, SMART,
Blocks etc)• SWISS-PROT/TrEMBL/RuleBase in Oracle
Standardized transfer of annotation from characterized proteins in
SWISS-PROT to TrEMBL entries
• TrEMBL entry is reliably recognized by a given method as a member of a certain group of proteins
• corresponding group of proteins in SWISS-PROT shares certain annotation
• common annotation is transferred to the TrEMBL entry and flagged as annotated by similarity
Automatic annotation information flow
• Get information necessary to assign proteins to groups eg using InterPro or other biological or family information- store in RuleBase
• Group proteins in SWISS-PROT by these conditions• Extract common annotation shared by all these proteins-
store in RuleBase• Group unannotated sequences by the conditions• Transfer common annotation flagged with evidence tags• Note: can add taxonomic constraints
Extract Reference Entries• Use XDB to extract entries from
standard database• Example:
Pfam:PF00509 HemagglutininHEMA_IAVI7/P03435HEMA_IANT6/P03436HEMA_IAAIC/P03437HEMA_IAX31/P03438HEMA_IAME2/P03439HEMA_IAEN7/P03440HEMA_IABAN/P03441HEMA_IADU3/P03442HEMA_IADA1/P03443HEMA_IADMA/P03444HEMA_IADM1/P03445HEMA_IADA2/P03446HEMA_IASH5/P03447
TrEMBLTrEMBLSWISS-PROTSWISS-PROT
PfamPfam
Extract Common Annotation132 entries read131 ID HEMA_XXXXX125 DE HEMAGGLUTININ PRECURSOR. 6 DE HEMAGGLUTININ.131 GN HA130 CC -!- FUNCTION: HEMAGGLUTININ IS RESPONSIBLE FOR ATTACHING THE130 CC VIRUS TO CELL RECEPTORS AND FOR INITIATING INFECTION.125 CC -!- SUBUNIT: HOMOTRIMER. EACH OF THE MONOMER IS FORMED BY TWO125 CC CHAINS (HA1 AND HA2) LINKED BY A DISULFIDE BOND. 75 DR HSSP; P03437; 1HGD. 31 DR HSSP; P03437; 1DLH.131 KW HEMAGGLUTININ; GLYCOPROTEIN; ENVELOPE PROTEIN102 KW SIGNAL 1 KW COAT PROTEIN; POLYPROTEIN; 3D-STRUCTURE130 FT CHAIN HA1 CHAIN.107 FT CHAIN HA2 CHAIN.102 FT SIGNAL
Store Common Annotation
• Store the used conditions and the extracted common annotation in a separate database
TrEMBLTrEMBLSWISS-PROTSWISS-PROT
XDBXDB
RuleBasRuleBasee
RULES
• Rules describe:– the content of the annotation to be transferred
(ACTIONS),– the CONDITIONS which the target TrEMBL entry
must fulfill in order to allow transfer of the annotation.
• Rules uniquely describe or delineate a set of SWISS-PROT entries.– The common annotation in these entries is transferred
to TrEMBL.
//#RULE RU000482#DATE 2001-01-11#USER OPS$WFL#PACK PROSITE?PSAC PS00449?EMOT PS00449!ECNO 3.6.1.34!SPDE ATP synthase A chain!CCFU KEY COMPONENT OF THE PROTON CHANNEL; IT MAY PLAY A DIRECT ROLE IN THE TRANSLOCATION OF PROTONS ACROSS THE MEMBRANE (BY SIMILARITY)!CCSU F-TYPE ATPASES HAVE 2 COMPONENTS, CF(1) - THE CATALYTIC CORE - AND CF(0) - THE MEMBRANE PROTON CHANNEL. CF(1) HAS FIVE SUBUNITS: ALPHA(3), BETA(3), GAMM A(1), DELTA(1), EPSILON(1). CF(0) HAS THREE MAIN SUBUNITS: A, B AND C (BY SIMILARITY)!CCLO INTEGRAL MEMBRANE PROTEIN (By Similarity)!CCSI TO THE ATPASE A CHAIN FAMILY!SPKW CF(0)!SPKW Hydrogen ion transport!SPKW Transmembrane//
CONDITIONS}ACTIONS
Add Annotation to Target
• Use conditions to extract entries from TrEMBL
• Add common annotation to the entries
TrEMBLTrEMBLSWISS-PROTSWISS-PROT
XDBXDB
RuleBasRuleBasee
Automatic annotation using multiple dbs
• Extract conditions from XDB
• Group SWISS-PROT by conditions
• Extract common annotation
• Group TrEMBL by conditions
• Add common annotation to TrEMBL
TrEMBLTrEMBLSWISS-PROTSWISS-PROT
PROSITEPROSITE
RuleBasRuleBasee
PfamPfam ENZYMEENZYME
INTERPROINTERPRO
Using tree structure of InterPro
RU000652 with additional condition connected by ‘AND’
//#RULE RU000652#DATE 2001-01-11#USER OPS$WFL#PACK PROSITE?IPRO IPR002379?PSAC PS00605?EMOT PS00605!SPDE ATP synthase C chain (Lipid-binding protein) (Subunit C)!ECNO 3.6.1.34!CCSU F-TYPE ATPASES HAVE 2 COMPONENTS, CF(1) - THE CATALYTIC CORE - AND CF(0) - THE MEMBRANE PROTON CHANNEL. CF(1) HAS FIVE SUBUNITS: ALPHA(3), BETA(3), GAMMA(1), DELTA(1), EPSILON(1). CF(0) HAS THREE MAIN SUBUNITS: A, B AND C (By Similarity)!CCSI TO THE ATPASE C CHAIN FAMILY!SPKW CF(0)!SPKW Hydrogen ion transport!SPKW Lipid-binding!SPKW Transmembrane//
Additional condition (parent signature)
Condition types• Signature hits:
- Prosite, Prints, Pfam, Prodom•Taxonomy:
- Broad groups like:ArchaeaBacteriophageEukaryotaProkaryotaEukaryotic viruses
- more specific such as species
•Organelle
•Conditions
•Negated conditions
Rule-building•Grouping and extraction of common annotation:
- semi automated but involves manual data-mining assisted by perl/shell scripts.
•Algorithmic data-mining: - fully automated.
- fast.- exhaustive exploration of condition-set/annotation
search-space . - non-biological, validity of rules being assessed by comparison with semi-manual approach.
Advantages of this method• Uses reliable ref database, prevents propagation of
incorrect annotation• Using common annotation of multiple entries, lower
over-prediction than from best hit of BLAST• Can standardize annotation and nomenclature of target
sequences, since reference is standardized• Can have different levels of common annotation from
different levels of family hierarchy • Independent of multi-domain organisation• Evidence tags allow for easy tracking and updating
Pitfalls of automatic functional analysis
• Multifunctional proteins- genome projects often assign single function, info is lost in homology search
• Hypothetical proteins (40% oRFs unknown), and poorly or even wrongly annotated proteins
• No coverage of position-specific annotation eg active sites
• Current methods provide only a phrase describing some properties of the unknown protein
It is important to have evidence for all annotation added
EVIDENCE TAGS
Predicting function from non-homology
• Look at position of genes relative to others, compare with other organisms
• Can still build up rules from annotated sequences using information you have on other features like fold, physical properties etc.
• Use physical properties and known attributes
Protein functions from regions
• Active sites- short, highly conserved regions
• Loops- charged residues and variable sequence
• Interior of protein- conservation of charged amino acids
• Polar (C,D,E,H,K,N,Q,R,S,T) - active sites
• Aromatic (F,H,W,Y) - protein ligand-binding sites
• Zn+-coord (C,D,E,H,N,Q) - active site, zinc finger
• Ca2+-coord (D,E,N,Q) - ligand-binding site
• Mg/Mn-coord (D,E,N,S,R,T) - Mg2+ or Mn2+ catalysis, ligand binding
• Ph-bind (H,K,R,S,T) - phosphate and sulphate binding
Protein functions from specific residues
• C disulphide-rich, metallo-thionein, zinc fingers
• DE acidic proteins (unknown)• G collagens• H histidine-rich glycoprotein• KR nuclear proteins, nuclear
localisation• P collagen, filaments• SR RNA binding motifs• ST mucins
Supplement annotation with Xrefs to other databases
• DDBJ/EMBL/GenBank Nucleotide Sequence Database
• PDB
• Genomic databases (FlyBase, MGD, SGD)
• 2D-Gel databases (ECO2DBASE, SWISS-2DPAGE, Aarhus/Ghent, YEPD, Harefield), Gene expression data
• Specialized collections (OMIM, InterPro, PROSITE, PRINTS, PFAM, ProDom, SMART, ENZYME, GPCRDB, Transfac, HSSP)
Approaches to functional annotation:
Automatic annotation (sequence homology, rules, transfer info from pdb)
Automatic classification (pattern databases, clustering, structure)
Automatic characterisation (functional databases) Context information (comparitive genome analysis, metabolic
pathway databases) Experimental results (2D gels, microarrays) Full manual annotation (SWISS-PROT style)
AUTOMATIC CLASSIFICATION
Annotation can by using Clustering methods eg CluSTR (EBI), and pattern searches (InterPro etc)- classification of proteins into different families
AUTOMATIC CHARACTERIZATION- FUNCTIONAL ANNOTATION SCHEMES
• First attempt –Riley classification of E.coli
• Genome sequencing projects driving force
• Need standardised system and vocabulary
• Functional schemes normally hierarchies of different levels of generalisation
Databases for Functional Information• KEGG -Kyoto encyclopedia of genes and genomes
– (http://www.genome.ad.jp/kegg/)
– Links genome information (GENES database) to high order functional information stored in PATHWAY database.
– Also has LIGAND database for chemical compounds, molecules and reactions.
• PEDANT -Protein Extraction, Description and Analysis Tool– (http://pedant.gsf.de/)
– Annotation for complete and incomplete genomes eg. List of ORFs, EC numbers, functional categories, list seqs with homologs, gene clusters, domain hits, TM, structure links, search facility for sequences etc
• WIT –What is there– ( http://www.cme.msu.edu/WIT)
– Database of metabolic pathways, can text search for ORFs, pathways, enzymes
• COG -Clusters of Orthologous Groups– (http://www.ncbi.nlm.nih.gov/COG)– Phylogenetic classification of proteins encoded in complete genomes. – Contains 2791 COGs including 30 genomes. – COGs thought to contain orthologous proteins, classified into broad functional
categories (transciption, replication, cell division). – COGNITOR assigns proteins to COGs based on best-hit, divides multi-domain
proteins– Can compare results with complete genomes, look for missing functions
• GO –Gene Ontology – (http://www.geneontology.org)– Standard vocabulary first used for mouse, fly and yeast– Three ontologies: molecular function, biological process and cellular
component
Databases for Functional Information (2)
Databases for Functional Information (3)• MIPS:MYGD FunCat –Functional catalogue (yeast)
http://www.mips.biochem.mpg.de/proj/yeast• EcoCyc -Encyclopedia of E. coli Genes and Metabolism
http://ecocyc.doubletwist.com/ecocyc/ecocyc.html• Enzyme database
http://wwwexpasy.ch/sprot/enzyme.html• TIGR –Gene identification list
http://www.tigr.org/tdb/mdb/mdb.html
All schemes have different depths, breadths and resolutions Schemes need to be applicable to all organisms, standardized
for comparisons and permit multiple assignments
Assignment of function
• Use a combination of databases, especially those with standardised functional information
• Search function databases with sequences to find matches -assign function eg PENDANT, PIR superfamilies, COGs, GO (via InterPro)
FUNCTIONAL CLASSIFICATION USING INTERPRO
• InterPro classification with 3-4 letter codes
• Mapping of InterPro entries to GO
• GO- Gene Ontology (SGD, FB & MGD) universal ontology for – molecular function– biological process– cellular component
Classification of IPRs
CGD Cell cycle/growth/death-CGDc cell cycle/division-CGDg cell growth/development-CGDd cell death
CYS Cytoskeletal/structural-CYSc cytoskeletal-CYSs structural-CYSv virus coat/capsid protein
DPT Defense/pathogenesis/toxin
DRG DNA/RNA-binding/regulation
DRM DNA/RNA metabolism-DRMr DNA repair/recombination-DRMp DNA replication-DRMm DNA/RNA modification-DRMt transcription/translation -DRMb ribosomal protein
MET Metabolism -METs substrate metabolism -METe electron transfer -METa amino acid metabolism -METn nucleic acid metabolism -METm metal binding proteins
OTH Other functions -OTHm cell motility -OTHt transposition -OTHa cell adhesion -OTHg miscellaneous functions -OTHh hormones -OTHi immune-response proteins -OTHf multifunctional proteins -OTHo multifunctional domains
PFD Protein folding & degradation -PFDc chaperone -PFDp protease/endopeptidase -PFDi protease inhibitor
PRG Protein-binding/other regulation -PRGg GPCRs -PRGr other receptors -PRGo other regulation
STD Signal transduction -STDk sig transduction kinases -STDp sig transduction phosphatases -STDr sig transduction response reg -STDs sig transduction sensors -STDc cell signalling
TRS Transport and secretion -TRSt transport (subtrates) -TRSi transport (ions) -TRSs secretion -TRSr carrier proteins
UNK Unknown function
Pie charts of whole proteome analysis of 4 organisms
Distribution of protein functions
Me
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M. tuberculosis
E. coli
B. subtilisS. cerevisae
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M. tuberculosis
E. coli
B. subtilis
S. cerevisae
GENOME ANNOTATION TOOLS
• Oakridge Genome Annotation Channel (http://compbio.ornl.gov/channel/)
• ENSEMBL (http://ensembl.ebi.ac.uk)• Artemis (http://www.sanger.ac.uk/Software/Artemis)
Sequence viewer and annotation tool• GeneQuiz (http//www.sander.ebi.ac.uk/genequiz/)
System for automated annotation of sequences, web access required
• Genome Annotation Assessment Project (GASP1) (http://www.fruitfly.org/GASP1)
PEDANT SYSTEM
Layer 1 bioinformatics tools
Layer 3 user interface to display results
Layer 2 database to store information -MySQL
parser of results
Programs written in Perl5 and some in C++ -portable. Processing of one sequence takes about 3 minutes
PSI-BLAST IMPALA
PREDATOR CLUSTALW
TMAP
SIGNALP SEG
PROSEARCH COILS
HMMER
MIPS PROSITE BLOCKS PIR COGS
Databases for searching
Manual annotation tool
Summary of protein sequence annotation
• Mask compositionally-biased and coiled-coil regions
• Identify transmembrane regions, signal peptides, GPI anchors
• Predict secondary structure
• Look for known domains from protein pattern databases
• Search sequence database for similar sequences
• If no or few results search with subsequences, do iterative searches
• Functional annotation: consider function of each domain present, annotation from database homologs, function from hits with 3D structure
SUMMARY OF ANNOTATION PIPELINE
NB look out for multi-domain proteins, put into genome context
Supplement with manual curation and
use evidence tags
NEW SEQUENCES FROM SEQUENCING PROJECT
NO SIGNIFICANT HITS
SIGNIFICANT HITS
PHYSICAL PROPERTIES, LOCALISATION ETC
NO SIGNIFICANT HITS
SIGNIFICANT HITS
PSI-BLAST
SEARCH FOR PATTERNS &
FUNCTION DBs
BLAST/ FASTA
IF EQUIVALOG, INFER FUNCTION
HIT TO 3D PROTEIN- STRUCTURE &
FUNCTION
ASSIGN PROTEIN FAMILY OR DOMAIN, CF OTHER PROTEINS
IN FAMILY, INFER FUNCTION
Search SCOP
• Predicting function from sequence requires another sequence to be mapped to a function –many hypothetical proteins in db and UPFs
• If sequence homologues are found, may not be functional homologues -qualitative rather than quantitative process- orthologues may have different functions
-enzyme homologues may be inactive
-equivalent functions may use different genes, not orthologue
• Analogy can infer molecular function, but not necessarily cellular function
LIMITS OF PROTEIN SEQUENCE ANALYSIS
LIMITS OF PROTEIN SEQUENCE ANALYSIS (2)
• Databases are biased in sequence and aa composition and search is dependent on size
• If no homology found- limited amount of information can be inferred
• Incorrect annotation can be propagated when similarity is over part on sequence not used in annotation
• No answers to tissue-specificity, binding of ligands, relationship between genotype and phenotype
LIMITS OF PROTEIN SEQUENCE ANALYSIS (3)
• Need additional information from experiments, eg can predict glycosylation sites, but not kind of sugar attached
• Problem with multidomain proteins (assign orthology on basis of domains or domain composition of whole protein?) -check also known domain architectures and their taxonomic limitations
Using different approaches to functional annotation: Status for SPTR
• Automatic annotation (RuleBase): 20% of all protein sequences/20% of all new sequences
• Automatic classification (InterPro, CluSTr, Structure): 60% of all protein sequences/60% of all new sequences
• Automatic characterisation (GO): 40% of all protein sequences/40% of all new sequences
• Full annotation (SWISS-PROT style): 20% of all protein sequences/5% of all new sequences
• Automatic annotation (RuleBase): 50% of all protein sequences in 2004
• Automatic classification (InterPro, CluSTr, Structure): 90% of all protein sequences in 2004
• Automatic characterisation (GO): 70% of all protein sequences in 2004
• Full annotation (SWISS-PROT style): 10% of all protein sequences in 2004
Using different approaches to functional annotation: Future for SPTR
IMPORTANT TO NOTE:
• DON’T COMPLETELY TRUST COMPUTER RESULTS
• CHECK LITERATURE
• CONFIRM WITH WETLAB WORK- mutational analysis gives valuable info about function
• COMPROMISE BETWEEN OVER AND UNDER-PREDICTIONS -overpredictions can be checked by curators, easier to delete than find missing info.