• NMFGO: Gene Function Prediction via Nonnegative Matrix Factorization with Gene Ontology

    3 days ago - By IEEE/ACM

    Gene Ontology is a controlled vocabulary of terms that describe molecule function, biological roles, and cellular locations of gene products , it hierarchically organizes more than 43,000 GO terms via the direct acyclic graph. A gene is generally annotated with several of these GO terms. Therefore, accurately predicting the association between genes and massive terms is a difficult challenge. To combat with this challenge, we propose an matrix factorization based approach called NMFGO. NMFGO stores the available GO annotations of genes in a gene-term association matrix and adopts an...
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  • Multi-Factored Gene-Gene Proximity Measures Exploiting Biological Knowledge Extracted from Gene Ontology: Application in Gene Clustering

    3 days ago - By IEEE/ACM

    To describe the cellular functions of proteins and genes, a potential dynamic vocabulary is Gene Ontology , which comprises of three sub-ontologies namely, Biological-process, Cellular-component, and Molecular-function. It has several applications in the field of bioinformatics like annotating/measuring gene-gene or protein-protein semantic similarity, identifying genes/proteins by their GO annotations for disease gene and target discovery, etc. To determine semantic similarity between genes, several semantic measures have been proposed in literature, which involve information content of...
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