Pathway Analysis & Ontology Flashcards
What is an ontology?
An ontology is a representation of knowledge, generally of a particular domain. It contains concepts which characterise the domain and is written using a standardised, structured syntax.
What do ontologies aim to provide?
A standardised means of description. Prevents problems with terms being used with different meanings and meanings having multiple terms. Ontologies enable a structural hierarchy of terms and can indicate relationships between terms and an ontologies properties. e.g. ** is a ** of **
What is an axiom?
Axioms are statments which are taken to be true i.e. b + a = a + b
In ontologies, axioms are assertions in a logical form.
The properties of relationships are a type of axiom
What are the aims of gene ontology?
Aims to unify the representation of a gene and gene products across all species by specifically
- Maintain and develop a controlled vocabulary of gene and gene product attributes.
- Annotate genes and gene products.
- Provide tools for east access to all aspect of project data and to enable functional interpretation of the data using GO, e.g. enrichment analysis
From which database is the human phenotype ontology derived?
OMIM
What are the issues with using human phenotype ontology in genetic analysis?
Phenotype terms work best when related to a small number of diseases otherwise it is not informative
What is Gene Set Enrichment Analysis (GSEA)?
Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states
What does Fishers exact T test calculate?
Fishers T test is a significance test which can be used for categorical data, i.e. determining whether there is a significant difference between two groups of data.
What is functional enrichment / over-representation analysis (ORA)?
This analysis looks for keywords or descriptors of the set of molecules of interest (e.g. those over-expressed) with respect to a background reference set (e.g. the whole genome/transcriptome/proteome/metabolome or the set of molecules detected by the technology employed) [1]. Classical enrichment analyses employ Fisher’s exact test, but many other enrichment methods have derived from it, e.g. hypergeometric, Kolmogorov–Smirnov or Wilcoxon statistical tests
What are metabolic network databases used for and name some examples.
Metabolic network databases are used for finding out the interactions between different proteins and in which pathways they operate.
Examples include KEGG, MetaCyc and STRING
What are network visualisation tools and name some examples?
Network visualisation tools are used for visualising molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other data.
Examples include Rectome and Cytoscape
What is a node and an edge?
A node the the component in a network visualisation which represents the gene/protein and the edge is a line representing the interaction between two nodes. Egges can represent predicted relationships or experimentally proven
What is SBML?
SMLB (Systems Biology Markup Language) is a representation format based on XML for storing and communicating computational models of biological processes.
