A novel network-based method for measuring the functional relationship between gene sets

作者：Wang, Qianghu; Sun, Jie; Zhou, Meng; Yang, Haixiu; Li, Yan; Li, Xiang; Lv, Sali; Li, Xia; Li, Yixue

来源：Bioinformatics, 2011, 27(11): 1521-1528.

DOI：10.1093/bioinformatics/btr154

• PROTEIN-PROTEIN INTERACTIONS
• CHRONIC LYMPHOCYTIC-LEUKEMIA
• CHRONIC MYELOID-LEUKEMIA
• ENRICHMENT ANALYSIS
• COMPREHENSIVE RESOURCE
• SEMANTIC SIMILARITY
• GENOMIC DATA
• P53 PATHWAY
• INFORMATION
• TOOL

Results: We introduce a novel network-based method, designated corrected cumulative rank score (CCRS), which analyzes the functional communication and physical interaction between genes, and presents an easy-to-use web-based toolkit called GsNetCom to quantify the functional relationship between two gene sets. To evaluate the performance of our method in assessing the functional similarity between two gene sets, we analyzed the functional coherence of complexes in functional catalog and identified protein complexes in the same functional catalog. The results suggested that CCRS can offer a significant advance in addressing the functional relationship between different gene sets compared with several other available tools or algorithms with similar functionality. We also conducted the case study based on our method, and succeeded in prioritizing candidate leukemia-associated protein complexes and expanding the prioritization and analysis of cancer-related complexes to other cancer types. In addition, GsNetCom provides a new insight into the communication between gene modules, such as exploring gene sets from the perspective of well-annotated protein complexes.

• 出版日期2011-6-1
• 单位哈尔滨医科大学; 中国科学院; 中国科学院上海生命科学研究院