title: A novel method to quantify gene set functional association based on gene ontology.
abstract: Numerous gene sets have been used as molecular signatures for exploring the genetic basis of complex disorders. These gene sets are distinct but related to each other in many cases; therefore, efforts have been made to compare gene sets for studies such as those evaluating the reproducibility of different experiments. Comparison in terms of biological function has been demonstrated to be helpful to biologists. We improved the measurement of semantic similarity to quantify the functional association between gene sets in the context of gene ontology and developed a web toolkit named Gene Set Functional Similarity (GSFS; http://bioinfo.hrbmu.edu.cn/GSFS). Validation based on protein complexes for which the functional associations are known demonstrated that the GSFS scores tend to be correlated with sequence similarity scores and that complexes with high GSFS scores tend to be involved in the same functional catalogue. Compared with the pairwise method and the annotation method, the GSFS shows better discrimination and more accurately reflects the known functional catalogues shared between complexes. Case studies comparing differentially expressed genes of prostate tumour samples from different microarray platforms and identifying coronary heart disease susceptibility pathways revealed that the method could contribute to future studies exploring the molecular basis of complex disorders.
authors: College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin, People's Republic of China.
authors: Sali
authors: S
authors: Lv
authors: Yan
authors: Y
authors: Li
authors: Qianghu
authors: Q
authors: Wang
authors: Shangwei
authors: S
authors: Ning
authors: Teng
authors: T
authors: Huang
authors: Peng
authors: P
authors: Wang
authors: Jie
authors: J
authors: Sun
authors: Yan
authors: Y
authors: Zheng
authors: Weisha
authors: W
authors: Liu
authors: Jing
authors: J
authors: Ai
authors: Xia
authors: X
authors: Li
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000502:physiology; D020022:Genetic Predisposition to Disease; D020407:Internet; D008957:Models, Genetic; D011506:Proteins / Q000378:metabolism*; D015203:Reproducibility of Results
chemical_list: D011506:Proteins