Protein Pathways and Pathway Databases

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Protein Pathways and Pathway Databases

• Shan Sundararaj
• University of Alberta
• Edmonton, AB
• ss23_at_ualberta.ca

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Interactions ? Networks ? Pathways

• A collection of interactions defines a network
• Pathways are a subset of networks
• All pathways are networks of interactions,
  however not all networks are pathways!
• Difference in the level of annotation/understandin
  g
• We can define a pathway as a biological network
  that relates to a known physiological process or
  phenotype

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Pathways

• However, there is no precise biological
  definition of a pathway
• Our partitioning of networks into pathways is
  somewhat arbitrary
• We choose the start/finish points based on
  important or easily understood compounds
• Gives us the ability to conceptualize the mapping
  of genotype ? phenotype

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Biological pathways

• There are 3 type of interactions that can be
  mapped to pathways
• 1) enzyme ligand
• metabolic pathways
• 2) protein protein
• cell signaling pathways
• complexes for cell processes
• 3) gene regulatory elements gene products
• genetic networks

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Pathways are inter-linked
Signalling pathway
Genetic network
STIMULUS
Metabolic pathway
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Metabolic Pathways
1993 Boehringer Mannheim GmbH - Biochemica
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What the pathway represents

• Metabolites involved
• Enzymes/transport proteins
• Order of reactions
• General biological function
• Reaction rates
• Expression data
• Inhibitors, activators, alternate pathways
• Genetic regulatory information

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Describing metabolic networks

• Classical biochemical pathways
• glycolysis, TCA cycle, etc.
• Stoichiometric modeling
• flux balance analysis, extreme pathways
• Kinetic modeling (CyberCell, E-cell, )
• Need to accumulate comprehensive kinetic
  information

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Complexity

• Pathways involve multiple enzymes, which may have
  multiple subunits, alternate forms, alternate
  specificities
• Enzymes may be involved in multiple pathways
• Malate dehydogenase appears in 6 different
  metabolic pathways in some databases

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Metabolic Pathway Reconstruction

• Given a genomic sequence, we can infer what
  metabolic pathways are available to an organism
• Used to design culture medium for Tropheryma
  whipplei by seeing what nutrients were essential
  for growth (Renesto et al., Lancet, 362, 447-449,
  2003)

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Co-expression within pathways

• Tempting thought genes that occur within the
  same pathway will show similar expression
  profiles
• Reality depends greatly on how you identify your
  pathways, KEGG pathways show at best 50
  co-expression in survey of available yeast
  expression data (Ihmels et al., Nat Biotechnol.
  22, 86-92, 2004).
• Expression levels do not correlate very well with
  protein interactions (unless they are stable
  complexes, maintained in many different
  conditions)

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Pathway Databases

• KEGG
• BioCyc
• Reactome
• GenMAPP
• BioCarta
• TransPATH
• 175 more at Pathway Resource List
  http//www.cbio.mskcc.org/prl/index.php

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BioPAX(www.biopax.org)

• Collaborative effort to create a data exchange
  format for biological pathway data

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KEGG

• 5904 chemical reactions
• 15,037 pathways
• 229 reference pathways
• 85 ortholog tables
• 181 organisms

http//www.genome.ad.jp/kegg/
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KEGG

• GENES Database
• The universe of genes and proteins in complete
  genomes
• LIGAND Database
• The universe of chemical reactions involving
  metabolites and other biochemical compounds
• Pathway Database
• Molecular interaction networks, metabolic and
  regulatory pathways, and molecular complexes

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Connection between KEGG and other Databases
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Pathways

• Represented as diagrams, manually created, stored
  as gifs
• Easy to link to, highlight genes of interest
• Generate orthologous pathways in other organisms

2.7.2.4 1.2.1.11 1.1.1.3 2.3.1.46 2.5.1.48 4.4.1.8
2.1.1.13 2.5.1.6
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http//www.biocyc.org/
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BioCyc

• The primary database was EcoCyc (E. coli)
• 21 more curated pathway/genome databases (PGDB),
  each focusing on one organism (e.g. HumanCyc)
• Also 142 more non-curated (computationally
  generated) pathways
• MetaCyc database contains non-redundant reference
  pathways from more than 240 organisms
• Supports Pathway Tools software suite to
  analyze PGDBs, and PathoLogic pathway
  prediction program for new genomes

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BioCyc

• Each PGDB includes info about
• Pathways, reactions, substrates
• Enzymes, transporters
• Genes, replicons
• Transcription factors, promoters, operons, DNA
  binding sites
• MetaCyc and EcoCyc are literature-based, the
  others are compu-tationally derived

Pathways
Reactions
Compounds
Proteins
Operons, Promoters, DNA Binding Sites
Genes
Chromosomes, Plasmids
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164 datasets
Query by protein, gene, compound, reaction,
pathway
BLAST sequence if protein name unknown
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MetaCyc Statistics
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EcoCyc Statistics
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BioCyc Pathway Tools
(Adapted from Pathway Tools tutorial,
http//bioinformatics.ai.sri.com/ptools/)

• Full Metabolic Map
• Paint gene expression data on metabolic network
  compare metabolic networks
• Pathways
• Pathway prediction (PathoLogic)
• Reactions
• Balance checker
• Compounds
• Chemical substructure comparison
• Enzymes,Transcription Factors
• Genes Blast search
• Operons
• Operon prediction

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PathoLogic Making PGDBs
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Completeness of Pathways
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Completeness of Pathways
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Issues with predicting pathways

• Predicting metabolic pathways from genome
• Predict genes
• Assign enzymatic function to genes
• Look for enzymes unique to pathway
• Check if pathway is balanced (no holes)
• Try to fill holes by re-searching genome

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Reactomehttp//www.reactome.org/
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Reactome

• Joint venture of CSHL and EBI (supercedes the
  Genome Knowledgebase project)
• Curated database of biological processes in
  humans
• Also rat, mouse, fugu, zebrafish, chicken
• Everything referenced by curators to literature
  citation or inference based on sequence
  similarity

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Reactome model

• Model reactions (input_entities)
  ?(output_entities)
• Distinguishes between modified/unmodified
  proteins (modification is an explicit reaction)
• Highly annotated at every step, very
  micromanaged, hope to find interesting links
  between reactions

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Reactome PathFinder

• Pathfinding between distant processes
• Enter two molecules or events and see if they can
  be joined together by reactions

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Reactome SkyPainter

• Find all reactions that contain a molecule or
  event
• Very flexible input, any one or more of
• protein/gene ID (UniProt, Genbank or others)
• protein/gene sequence
• GO or OMIM identifier
• time series from a gene expression study

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Reactome SkyPainter

• Starry sky output
• If expression data used, you get different
  colours for different levels of expression
• If time series available, you can make an
  animation

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GenMAPP(www.genmapp.org)

• Designed to rapidly analyze gene profiling data
  in the context of known biochemical pathways
• Pathways (MAPPs) are authored by experts, as well
  as adapting several pathways from KEGG
• Pathways easily web-queryable
• Free for all users
• But Windows platform only

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GenMAPP

• Easy to draw/edit pathways
• Color genes from user imported expression data

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MAPPFinder maps to GO ontology
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BioCarta(www.biocarta.com)
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BioCarta

• Not a public database, but offers free,
  clickable, graphics-rich pathway database and
  gene information
• Community annotation
• Easy to use glyph system for genes
• 355 pathways
• mostly human/mouse metabolic and signaling
  pathways

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TransPATH
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TransPATH

• Part of larger BioBase package (commercial)
• PathwayBuilder package for network visualization
• Highly integrated with signaling networks and
  transcription factor networks (TransFAC)
• Linked to extensive enzyme information in BRENDA
  (www.brenda.uni-koeln.de/)
• 28,456 molecules 52,007 reactions 54 hand-drawn
  pathways

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Pathway Database Comparison
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Conclusion

• Pathway databases are continually evolving, and
  are an important abstract mid-level of expressing
  data between genes/proteins and observable
  phenotypes
• Metabolic pathways are most well studied/modeled
• Many different formats of storage and display,
  but moving towards standards (PSI-MI, Biopax)