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GOSAP: Gene Ontology Based Semantic Alignment of Biological Pathways
Högskolan i Skövde, Institutionen för kommunikation och information.
Högskolan i Skövde, Institutionen för kommunikation och information.
2005 (engelsk)Rapport (Annet vitenskapelig)
Abstract [en]

A large number of biological pathways have been assembled in later years, and are being stored in databases. Hence, the need for methods to analyse these pathways has emerged. One class of methods compares pathways, in order to discover parts that are evolutionary conserved between species or to discover intra-species similarites. Most previous work has been focused on methods targeted at metabolic pathways utilising the EC enzyme hierarchy. Here, we propose a Gene Ontology (GO) based approach for finding semantic local alignments when comparing paths in biological pathways where the nodes are gene products. The method takes advantage of all three sub-ontologies, and uses a measure of semantic similarity to calculate a match score between gene products. Our proposed method is applicable to all types of biological pathways, where nodes are gene products, e.g. regulatory pathways, signalling pathways and metabolic enzyme-to-enzyme pathways. It would also be possible to extend the method to work with other types of nodes, as long as there is an ontology or abstraction hierarchy available for categorising the nodes. We demonstrate that the method is useful for studying protein regulatory pathways in S. cerevisiae, as well as metabolic pathways for the same organism.

sted, utgiver, år, opplag, sider
Skövde: Institutionen för kommunikation och information , 2005. , s. 8
Serie
IKI Technical Reports ; HS-IKI-TR-05-005
HSV kategori
Identifikatorer
URN: urn:nbn:se:his:diva-1260OAI: oai:DiVA.org:his-1260DiVA, id: diva2:2396
Tilgjengelig fra: 2008-06-17 Laget: 2008-06-17 Sist oppdatert: 2018-01-13bibliografisk kontrollert

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