Download JunlClub_June13 - Mouse Genome Informatics

Ontology annotation: mapping genomic regions
biological function
Paul D Thomas, Huaiyu Mi and Suzanna Lewis
Ontologies
GO 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 sequence
evolution data with expanded representation
biological 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:
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Pathway
Molecule
Reaction
Cell type or subcellular component