A network-based gene-weighting approach for pathway analysis
文献类型：期刊论文
| 作者 | Fang, ZY; Tian, WD; Ji, HB |
| 刊名 | CELL RESEARCH
 |
| 出版日期 | 2012 |
| 卷号 | 22期号:3页码:565-580 |
| 关键词 | gene weighting functional association network pathway analysis gene set analysis gene expression microarray multi-subunit protein |
| 通讯作者 | Ji, HB (reprint author), Chinese Acad Sci, Inst Biochem & Cell Biol, State Key Lab Cell Biol, SIBS, Shanghai 200031, Peoples R China.,weidong.tian@fudan.edu.cn ; hbji@sibs.ac.cn |
| 英文摘要 | Classical algorithms aiming at identifying biological pathways significantly related to studying conditions frequently reduced pathways to gene sets, with an obvious ignorance of the constitutive non-equivalence of various genes within a defined pathway. We here designed a network-based method to determine such non-equivalence in terms of gene weights. The gene weights determined are biologically consistent and robust to network perturbations. By integrating the gene weights into the classical gene set analysis, with a subsequent correction for the "over-counting" bias associated with multi-subunit proteins, we have developed a novel gene-weighed pathway analysis approach, as implemented in an R package called "Gene Associaqtion Network-based Pathway Analysis" (GANPA). Through analysis of several microarray datasets, including the p53 dataset, asthma dataset and three breast cancer datasets, we demonstrated that our approach is biologically reliable and reproducible, and therefore helpful for microarray data interpretation and hypothesis generation. |
| 学科主题 | Cell Biology |
| 类目[WOS] | Cell Biology |
| 关键词[WOS] | ENDOTHELIAL GROWTH-FACTOR ; WIDE EXPRESSION PROFILES ; PROBE LEVEL DATA ; SET ENRICHMENT ; TESTING ASSOCIATION ; BIOLOGICAL PATHWAYS ; GLOBAL TEST ; CELL-CYCLE ; CANCER ; IDENTIFICATION |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000300942400013 |
| 版本 | 出版稿 |
| 源URL | [http://202.127.25.143/handle/331003/561]  |
| 专题 | 上海生化细胞研究所_上海生科院生化细胞研究所 |
| 推荐引用方式 GB/T 7714 | Fang, ZY,Tian, WD,Ji, HB. A network-based gene-weighting approach for pathway analysis[J]. CELL RESEARCH,2012,22(3):565-580. |
| APA | Fang, ZY,Tian, WD,&Ji, HB.(2012).A network-based gene-weighting approach for pathway analysis.CELL RESEARCH,22(3),565-580. |
| MLA | Fang, ZY,et al."A network-based gene-weighting approach for pathway analysis".CELL RESEARCH 22.3(2012):565-580. |
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