Advancing Science with DNA Sequence

IMG terms and pathwaysKrishna Krishna

PalaniappanPalaniappan

Amy ChenAmy Chen

Frank Frank KorzeniewskiKorzeniewski

Yuri GrechkinYuri Grechkin

Ernest SzetoErnest Szeto

Victor MarkowitzVictor Markowitz

Natalia IvanovaNatalia Ivanova

Iain AndersonIain Anderson

Thanos LykidisThanos Lykidis

Nikos KyrpidesNikos Kyrpides

MGM WorkshopMGM Workshop

February 1, 2012February 1, 2012

Advancing Science with DNA Sequence

Why so many?What’s the difference?Which one should I use?

New: SEED subsystemsTransport DB, Phenotypes

Advancing Science with DNA Sequence

Where it all comes from

• Experimental data: gene A in a genome X

catalyzes a reaction interacts with another protein(s) gene knock-out causes certain phenotype …

This information is recorded in a structured way: ontologies (e.g. Gene Ontology) pathway collections (metabolic and

protein-protein interaction) other (reasoning rules, like TIGR

Genome Properties)

Advancing Science with DNA Sequence

Modeling the data properly – why nobody does that

• Genes are connected to phenotypes via a multi-step process, with many parameters

• We have very vague ideas about the steps/parameters for the majority of genes/phenotypes

• If we design a relational database for gene/phenotype connections, most tables will be empty

gene phenotype

transcript

proteinenzyme

reaction

pathway

compoundsevidence

Advancing Science with DNA Sequence

What it looks like in real life – KEGG vs MetaCyc

KEGG

http://www.genome.jp/kegg/

MetaCyc

http://metacyc.org/

Advancing Science with DNA Sequence

Ammonia oxidation pathway in KEGG

Advancing Science with DNA Sequence

The same pathway/reaction in MetaCyc

Advancing Science with DNA Sequence

Even MetaCyc record is still incomplete

• Which subunit has which cofactor?

• Type of Cu2+ cluster, type of Fe2+ cluster?

• One of the subunits is a cytochrome c, yet the enzyme is cytosolic?

• Does it require any help with maturation of metal clusters?

• Pseudomonas sp. PB16 was shown to have only 1 enzyme from the pathway, hydroxylamine reductase. Does it have the entire pathway?

Advancing Science with DNA Sequence

Even bigger mess: bioinformatics inference

• Experimental data: gene A in a genome X

catalyzes a reaction interacts with another protein(s) gene knock-out causes certain phenotype …

What about gene B in genome Y, which is similar to gene A?

Advancing Science with DNA Sequence

“True or false?” game

• If gene B was manually annotated, the annotation must be correct

• If gene B was manually annotated, and it has a bi-directional best BLAST hit to gene A with e-value of 1.0e-5, the annotation must be correct

• If gene B was manually annotated, and it has >50% identity to gene A, it is found in the same conserved chromosomal neighborhood as gene A, the annotation must be correct

• …

Advancing Science with DNA Sequence

Poorly done inference - MetaCyc

• Software called PathoLogic• Parses annotated files, tries to find matches

between EC numbers/full product names/partial product names and reactions in MetaCyc database

• Automatically infers pathway presence based on matches to MetaCyc reactions

• Tries to find candidate genes for “missing” enzymes by doing BLAST of the genes assigned to this reaction in other organisms

• Generates a lot of false positives - inferred the presence of ammonia oxidation pathway in Staphylococcus based on the presence of 1 gene annotated as ammonia monooxygenase in GenBank file

Advancing Science with DNA Sequence

Better inference: KEGG

• Annotation is inferred based on orthology, defined as bi-directional best BLAST hits, manually refined based on “Ortholog tables” and chromosomal clusters

• Poorly documented, but seems to generate a lot less false positives than PathoLogic

Advancing Science with DNA Sequence

Even the best structured inference is far from perfect

• Problem: both BLAST or Smith-Waterman don’t know which amino acids are more important for protein function than others

• Using consensus sequence (either as PSSM or HMM) with family-specific bit score cutoffs would be much better

Advancing Science with DNA Sequence

Pathway collections: KEGG, MetaCyc and others

Which particular set of interactions is a pathway? (i. e. how do we define pathway boundaries within the network?)

Advancing Science with DNA Sequence

Ideal solution: pathway NR

• All pathway collections share a common skeleton of reactions, which consist of reactants (compounds)

• All reactions share the common base of proteins annotated as catalysts

• Can we merge the information from different collections, using the best features of all of them?

Advancing Science with DNA Sequence

IMG terms: 3 types

IMG terms of 3 types:1. gene product2. multi-subunit protein complex3. modified protein

A BR1

Enzyme (EC x.x.x.x)

Enzyme (EC x.x.x.x)monomeric, needs

cofactor C

Enzyme (EC x.x.x.x)heterotrimeric, needs cofactor D

Enzyme (EC x.x.x.x)monomeric precursor

R2, spontaneousC

Enzyme (EC x.x.x.x)heterotrimeric, subunit B

Enzyme (EC x.x.x.x)heterotrimeric, subunit C

R4, chaperone

Enzyme (EC x.x.x.x)heterotrimeric, subunit A precursor

D R3, spontaneous

Enzyme (EC x.x.x.x)heterotrimeric, subunit A

IMG term of the type “Modified protein”

Not an IMG term!

IMG term of the type “Protein complex”

IMG term of the type “Gene product”

IMG term of the type “Gene product”

Advancing Science with DNA SequenceProtein-protein interaction pathways: same model

Advancing Science with DNA Sequence

You’ve been warned!