Bayesian Data Integration and Enrichment Analysis for Predicting Gene Function in Malaria
CiE '09 Proceedings of the 5th Conference on Computability in Europe: Mathematical Theory and Computational Practice
Inferring protein interactions from sequence using support vector machine
IJCNN'09 Proceedings of the 2009 international joint conference on Neural Networks
Computing with words with the ontological self-organizing map
IEEE Transactions on Fuzzy Systems - Special section on computing with words
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
A feature and information theoretic framework for semantic similarity and relatedness
ISWC'10 Proceedings of the 9th international semantic web conference on The semantic web - Volume Part I
WF-MSB: A weighted fuzzy-based biclustering method for gene expression data
International Journal of Data Mining and Bioinformatics
Research Article: Large-scale mining co-expressed genes in Arabidopsis anther: From pair to group
Computational Biology and Chemistry
Ontology-based resources for bioinformatics analysis
International Journal of Metadata, Semantics and Ontologies
Finding disease similarity based on implicit semantic similarity
Journal of Biomedical Informatics
SEMCCO'11 Proceedings of the Second international conference on Swarm, Evolutionary, and Memetic Computing - Volume Part II
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Finding cross genome patterns in annotation graphs
DILS'12 Proceedings of the 8th international conference on Data Integration in the Life Sciences
Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Improving recommendation performance through ontology-based semantic similarity
ICICA'12 Proceedings of the Third international conference on Information Computing and Applications
Ontology-Based genes similarity calculation with TF-IDF
ICICA'12 Proceedings of the Third international conference on Information Computing and Applications
Integration of Literature with Heterogeneous Information for Genes Correlation Scoring
ACM Journal on Emerging Technologies in Computing Systems (JETC) - Special Issue on Bioinformatics
Measuring Relatedness Between Scientific Entities in Annotation Datasets
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
GOtoGene: a method for determining the functional similarity among gene products
AusDM '12 Proceedings of the Tenth Australasian Data Mining Conference - Volume 134
Hi-index | 3.84 |
Motivation: Although controlled biochemical or biological vocabularies, such as Gene Ontology (GO) ( http://www.geneontology.org), address the need for consistent descriptions of genes in different data sources, there is still no effective method to determine the functional similarities of genes based on gene annotation information from heterogeneous data sources. Results: To address this critical need, we proposed a novel method to encode a GO term's semantics (biological meanings) into a numeric value by aggregating the semantic contributions of their ancestor terms (including this specific term) in the GO graph and, in turn, designed an algorithm to measure the semantic similarity of GO terms. Based on the semantic similarities of GO terms used for gene annotation, we designed a new algorithm to measure the functional similarity of genes. The results of using our algorithm to measure the functional similarities of genes in pathways retrieved from the saccharomyces genome database (SGD), and the outcomes of clustering these genes based on the similarity values obtained by our algorithm are shown to be consistent with human perspectives. Furthermore, we developed a set of online tools for gene similarity measurement and knowledge discovery. Availability: The online tools are available at: http://bioinformatics.clemson.edu/G-SESAME Contact: jzwang@cs.clemson.edu Supplementary information: http://bioinformatics.clemson.edu/Publication/Supplement/gsp.htm