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SOP for pathway inference in Integrated Microbial Genomes (IMG).

Anderson I, Chen A, Markowitz V, Kyrpides N, Ivanova N - Stand Genomic Sci (2011)

Bottom Line: The three categories of pathway assertion are asserted (likely present), not asserted (likely absent), and unknown.In the unknown category, at least one term necessary for the pathway is missing, but an ortholog in another organism has the corresponding term assigned to it.Automatic pathway inference is an important initial step in genome analysis.

View Article: PubMed Central - PubMed

Affiliation: DOE Joint Genome Institute, Walnut Creek, CA, USA.

ABSTRACT
One of the most important aspects of genomic analysis is the prediction of which pathways, both metabolic and non-metabolic, are present in an organism. In IMG, this is carried out by the assignment of IMG terms, which are organized into IMG pathways. Based on manual and automatic assignment of IMG terms, the presence or absence of IMG pathways is automatically inferred. The three categories of pathway assertion are asserted (likely present), not asserted (likely absent), and unknown. In the unknown category, at least one term necessary for the pathway is missing, but an ortholog in another organism has the corresponding term assigned to it. Automatic pathway inference is an important initial step in genome analysis.

No MeSH data available.


Related in: MedlinePlus

Partial list of genomes from a Pathway Details page showing the number of genes associated with the pathway and the pathway assertion status.
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f2: Partial list of genomes from a Pathway Details page showing the number of genes associated with the pathway and the pathway assertion status.

Mentions: IMG terms participate as catalysts in IMG reactions, which make up IMG pathways. Some IMG reactions are traditional biochemical reactions corresponding to conversion of small molecules with known stoichiometry, while others describe chemical conversions of unknown or undefined stoichiometry, transport of small molecules or macromolecules, protein-protein interactions or other interactions between other macromolecules, such as conformational changes (see BioPax documentation for detailed classification of reactions, [2]). Figure 1 shows the top section of a Pathway Details page with the list of reactions and the terms that act as catalysts for these reactions. The example shown is a non-metabolic pathway, which consists of protein-protein and protein-DNA interactions, as well as topological changes of DNA, as described in the reaction definitions. For a metabolic pathway, the reaction definition would be a biochemical reaction. The bottom section of a Pathway Details page shows a list of organisms, how many genes they have that belong to the pathway, and the pathway assertion status (Figure 2).


SOP for pathway inference in Integrated Microbial Genomes (IMG).

Anderson I, Chen A, Markowitz V, Kyrpides N, Ivanova N - Stand Genomic Sci (2011)

Partial list of genomes from a Pathway Details page showing the number of genes associated with the pathway and the pathway assertion status.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368422&req=5

f2: Partial list of genomes from a Pathway Details page showing the number of genes associated with the pathway and the pathway assertion status.
Mentions: IMG terms participate as catalysts in IMG reactions, which make up IMG pathways. Some IMG reactions are traditional biochemical reactions corresponding to conversion of small molecules with known stoichiometry, while others describe chemical conversions of unknown or undefined stoichiometry, transport of small molecules or macromolecules, protein-protein interactions or other interactions between other macromolecules, such as conformational changes (see BioPax documentation for detailed classification of reactions, [2]). Figure 1 shows the top section of a Pathway Details page with the list of reactions and the terms that act as catalysts for these reactions. The example shown is a non-metabolic pathway, which consists of protein-protein and protein-DNA interactions, as well as topological changes of DNA, as described in the reaction definitions. For a metabolic pathway, the reaction definition would be a biochemical reaction. The bottom section of a Pathway Details page shows a list of organisms, how many genes they have that belong to the pathway, and the pathway assertion status (Figure 2).

Bottom Line: The three categories of pathway assertion are asserted (likely present), not asserted (likely absent), and unknown.In the unknown category, at least one term necessary for the pathway is missing, but an ortholog in another organism has the corresponding term assigned to it.Automatic pathway inference is an important initial step in genome analysis.

View Article: PubMed Central - PubMed

Affiliation: DOE Joint Genome Institute, Walnut Creek, CA, USA.

ABSTRACT
One of the most important aspects of genomic analysis is the prediction of which pathways, both metabolic and non-metabolic, are present in an organism. In IMG, this is carried out by the assignment of IMG terms, which are organized into IMG pathways. Based on manual and automatic assignment of IMG terms, the presence or absence of IMG pathways is automatically inferred. The three categories of pathway assertion are asserted (likely present), not asserted (likely absent), and unknown. In the unknown category, at least one term necessary for the pathway is missing, but an ortholog in another organism has the corresponding term assigned to it. Automatic pathway inference is an important initial step in genome analysis.

No MeSH data available.


Related in: MedlinePlus