Bioinformatics (Oxford, England) · 2016
Tissue-specific pathway association analysis using genome-wide association study summaries.
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Wang Wenyu, Hao Jingcan, Zheng Shuyu, Fan Qianrui, He Awen, Wen Yan, Guo Xiong, Wu Cuiyan, Wang Sen, Yang Tielin, Shen Hui, Chen Xiangding, Tian Qing, Tan Lijun, Deng Hong-Wen, Zhang Feng
Аннотация
MOTIVATION: Pathway association analysis has made great achievements in elucidating the genetic basis of human complex diseases. However, current pathway association analysis approaches fail to consider tissue-specificity.
RESULTS: We developed a tissue-specific pathway interaction enrichment analysis algorithm (TPIEA). TPIEA was applied to two large Caucasian and Chinese genome-wide association study summary datasets of bone mineral density (BMD). TPIEA identified several significant pathways for BMD [false discovery rate (FDR) < 0.05], such as KEGG FOCAL ADHESION and KEGG AXON GUIDANCE, which had been demonstrated to be involved in the development of osteoporosis. We also compared the performance of TPIEA and classical pathway enrichment analysis, and TPIEA presented improved performance in recognizing disease relevant pathways. TPIEA may help to fill the gap of classic pathway association analysis approaches by considering tissue specificity.
AVAILABILITY AND IMPLEMENTATION: The online web tool of TPIEA is available at https://sourceforge.net/projects/tpieav1/files CONTACT: fzhxjtu@mail.xjtu.edu.cnSupplementary information: Supplementary data are available at Bioinformatics online.
RESULTS: We developed a tissue-specific pathway interaction enrichment analysis algorithm (TPIEA). TPIEA was applied to two large Caucasian and Chinese genome-wide association study summary datasets of bone mineral density (BMD). TPIEA identified several significant pathways for BMD [false discovery rate (FDR) < 0.05], such as KEGG FOCAL ADHESION and KEGG AXON GUIDANCE, which had been demonstrated to be involved in the development of osteoporosis. We also compared the performance of TPIEA and classical pathway enrichment analysis, and TPIEA presented improved performance in recognizing disease relevant pathways. TPIEA may help to fill the gap of classic pathway association analysis approaches by considering tissue specificity.
AVAILABILITY AND IMPLEMENTATION: The online web tool of TPIEA is available at https://sourceforge.net/projects/tpieav1/files CONTACT: fzhxjtu@mail.xjtu.edu.cnSupplementary information: Supplementary data are available at Bioinformatics online.