Ontology annotation: mapping genomic regions

biological functionPaul D Thomas, Huaiyu Mi and Suzanna

Lewis

OntologiesGO represents function from the gene’s eye view, in relation to a large and growing context of biological knowledge at all levels. Focus is on representing the structure and context of general biological knowledge.

Pathway ontologies represent function from the point of view of biochemical reactions and interactions, which are ordered into networks and causal cascades. Has the capability to represent details including molecular mechanisms, and the representation of temporal ordering of events.

Pathway ontologies provide detailed biochemical relationships between molecular types; these relationships are complementary to the representation in the Gene Ontology, and, indeed, can be explicitly connected to Gene Ontology terms.

Annotations

GO evidence: – Literature-based– Homology-based – actually a statement about the

function of the most recent common ancestor and the inheritance of function from that ancestor

– Computational

Annotations

The reliability of the homology-based annotation depends on the reliability of the two links in the inference chain: the literature-based inference for the function of one gene, and the inference of descent from a common ancestor… Either of these links can be human curated or computationally inferred…

Curator-reviewed BLAST searching has been shown to result in less reliable GO annotations than phylogenetic tree building algorithms and curated subfamily hidden Markov models.

Annotations

GO evidence: – Literature-based– Homology-based – actually a statement about the

function of the most recent common ancestor and the inheritance of function from that ancestor

– Computational

The PANTHER pathway database uses the GO evidence codes for direct evidence and links to ancestral nodes in phylogenetic trees to trace homology inferences

PANTHER version 6: protein sequenceevolution data with expanded

representationbiological pathways

Huaiyu Mi, Nan Guo, Anish Kejariwal and Paul D. Thomas

PANTHER• PANTHER family and subfamily models have

been used to classify all (?) known and predicted protein coding genes in the human, mouse, rat and Drosophila genomes

• Each subtree should contain as many sequences as possible having the same label (?)

• Classes: – Pathway– Molecule– Reaction– Cell type or subcellular component