Methodological Review: Towards knowledge-based gene expression data mining
Journal of Biomedical Informatics
Journal of Biomedical Informatics
Inferring protein interactions from sequence using support vector machine
IJCNN'09 Proceedings of the 2009 international joint conference on Neural Networks
Computers in Biology and Medicine
Finding top-k similar pairs of objects annotated with terms from an ontology
SSDBM'10 Proceedings of the 22nd international conference on Scientific and statistical database management
Towards a framework for developing semantic relatedness reference standards
Journal of Biomedical Informatics
Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium
Finding disease similarity based on implicit semantic similarity
Journal of Biomedical Informatics
An Overview on Semantic Analysis of Proteomics Data
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
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Motivation: Pathway modeling requires the integration of multiple data including prior knowledge. In this study, we quantitatively assess the application of Gene Ontology (GO)-derived similarity measures for the characterization of direct and indirect interactions within human regulatory pathways. The characterization would help the integration of prior pathway knowledge for the modeling. Results: Our analysis indicates information content-based measures outperform graph structure-based measures for stratifying protein interactions. Measures in terms of GO biological process and molecular function annotations can be used alone or together for the validation of protein interactions involved in the pathways. However, GO cellular component-derived measures may not have the ability to separate true positives from noise. Furthermore, we demonstrate that the functional similarity of proteins within known regulatory pathways decays rapidly as the path length between two proteins increases. Several logistic regression models are built to estimate the confidence of both direct and indirect interactions within a pathway, which may be used to score putative pathways inferred from a scaffold of molecular interactions. Contact: s.guo@wriwindber.org