InforLorV4, Main, Exploration, bibRecord, 001D13

Functional classification of genes using semantic distance and fuzzy clustering approach: evaluation with reference sets and overlap analysis.

Identifieur interne : 001D13 ( Main/Exploration ); précédent : 001D12; suivant : 001D14

Functional classification of genes using semantic distance and fuzzy clustering approach: evaluation with reference sets and overlap analysis.

Auteurs : Marie-Dominique Devignes [France] ; Sidahmed Benabderrahmane ; Malika Smaïl-Tabbone ; Amedeo Napoli ; Olivier Poch

Source :

International journal of computational biology and drug design [ 1756-0756 ] ; 2012.

RBID : pubmed:23013652

Descripteurs français

KwdFr :
- Algorithmes, Analyse de regroupements, Bases de données génétiques, Famille multigénique, Humains, Logique floue, Tests de criblage à haut débit ().
MESH :
- Algorithmes, Analyse de regroupements, Bases de données génétiques, Famille multigénique, Humains, Logique floue, Tests de criblage à haut débit.

English descriptors

KwdEn :
- Algorithms, Cluster Analysis, Databases, Genetic, Fuzzy Logic, High-Throughput Screening Assays (methods), Humans, Multigene Family.
MESH :
- methods : High-Throughput Screening Assays.
- Algorithms, Cluster Analysis, Databases, Genetic, Fuzzy Logic, Humans, Multigene Family.

Abstract

Functional classification aims at grouping genes according to their molecular function or the biological process they participate in. Evaluating the validity of such unsupervised gene classification remains a challenge given the variety of distance measures and classification algorithms that can be used. We evaluate here functional classification of genes with the help of reference sets: KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathways and Pfam clans. These sets represent ground truth for any distance based on GO (Gene Ontology) biological process and molecular function annotations respectively. Overlaps between clusters and reference sets are estimated by the F-score method. We test our previously described IntelliGO semantic distance with hierarchical and fuzzy C-means clustering and we compare results with the state-of-the-art DAVID (Database for Annotation Visualisation and Integrated Discovery) functional classification method. Finally, study of best matching clusters to reference sets leads us to propose a set-difference method for discovering missing information.

DOI: 10.1504/IJCBDD.2012.049207
PubMed: 23013652

Affiliations:

France

Le document en format XML

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<front><div type="abstract" xml:lang="en">Functional classification aims at grouping genes according to their molecular function or the biological process they participate in. Evaluating the validity of such unsupervised gene classification remains a challenge given the variety of distance measures and classification algorithms that can be used. We evaluate here functional classification of genes with the help of reference sets: KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathways and Pfam clans. These sets represent ground truth for any distance based on GO (Gene Ontology) biological process and molecular function annotations respectively. Overlaps between clusters and reference sets are estimated by the F-score method. We test our previously described IntelliGO semantic distance with hierarchical and fuzzy C-means clustering and we compare results with the state-of-the-art DAVID (Database for Annotation Visualisation and Integrated Discovery) functional classification method. Finally, study of best matching clusters to reference sets leads us to propose a set-difference method for discovering missing information.</div>
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Functional classification of genes using semantic distance and fuzzy clustering approach: evaluation with reference sets and overlap analysis.

Functional classification of genes using semantic distance and fuzzy clustering approach: evaluation with reference sets and overlap analysis.

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki

	Serveur d'exploration sur la recherche en informatique en Lorraine
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