slepr a sample-level enrichment-based pathway ranking method — seeking biological themes through pathway-level consistencyslepr一sample-level enrichment-based路径排序法u2014u2014通过pathway-level寻求生物主题一致性.pdfVIP

下载本文档

3
0
约13.76万字
约 17页
2017-09-12 发布于上海
举报
版权申诉

slepr a sample-level enrichment-based pathway ranking method — seeking biological themes through pathway-level consistencyslepr一sample-level enrichment-based路径排序法u2014u2014通过pathway-level寻求生物主题一致性.pdf

1、本文档共17页，可阅读全部内容。
2、原创力文档（book118）网站文档一经付费（服务费），不意味着购买了该文档的版权，仅供个人/单位学习、研究之用，不得用于商业用途，未经授权，严禁复制、发行、汇编、翻译或者网络传播等，侵权必究。
3、本站所有内容均由合作方或网友上传，本站不对文档的完整性、权威性及其观点立场正确性做任何保证或承诺！文档内容仅供研究参考，付费前请自行鉴别。如您付费，意味着您自己接受本站规则且自行承担风险，本站不退款、不进行额外附加服务；查看《如何避免下载的几个坑》。如果您已付费下载过本站文档，您可以点击这里二次下载。
4、如文档侵犯商业秘密、侵犯著作权、侵犯人身权等，请点击“版权申诉”（推荐），也可以打举报电话：400-050-0827(电话支持时间：9:00-18:30)。
5、该文档为VIP文档，如果想要下载，成为VIP会员后，下载免费。
6、成为VIP后，下载本文档将扣除1次下载权益。下载后，不支持退款、换文档。如有疑问请联系我们。
7、成为VIP后，您将拥有八大权益，权益包括：VIP文档下载权益、阅读免打扰、文档格式转换、高级专利检索、专属身份标志、高级客服、多端互通、版权登记。
8、VIP文档为合作方或网友上传，每下载1次，网站将根据用户上传文档的质量评分、类型等，对文档贡献者给予高额补贴、流量扶持。如果你也想贡献VIP文档。上传文档

slepr a sample-level enrichment-based pathway ranking method — seeking biological themes through pathway-level consistencyslepr一sample-level enrichment-based路径排序法u2014u2014通过pathway-level寻求生物主题一致性

SLEPR: A Sample-Level Enrichment-Based Pathway Ranking Method — Seeking Biological Themes through Pathway-Level Consistency Ming Yi, Robert M. Stephens* Advanced Biomedical Computing Center, Advanced Technology Program, SAIC-Frederick Inc., NCI-Frederick, Frederick, Maryland, United States of America Abstract Analysis of microarray and other high throughput data often involves identification of genes consistently up or down- regulated across samples as the first step in extraction of biological meaning. This gene-level paradigm can be limited as a result of valid sample fluctuations and biological complexities. In this report, we describe a novel method, SLEPR, which eliminates this limitation by relying on pathway-level consistencies. Our method first selects the sample-level differentiated genes from each individual sample, capturing genes missed by other analysis methods, ascertains the enrichment levels of associated pathways from each of those lists, and then ranks annotated pathways based on the consistency of enrichment levels of individual samples from both sample classes. As a proof of concept, we have used this method to analyze three public microarray datasets with a direct comparison with the GSEA method, one of the most popular pathway-level analysis methods in the field. We found that our method was able to reproduce the earlier observations with significant improvements in depth of coverage for validated or expected biological themes, but also produced additional insights that make biological sense. This new method extends existing analyses approaches and facilitates integration of different types of HTP data. Citation: Yi M, Stephens RM (2008) SLEPR: A Sample-Level Enrichment-Based Pathway Ranking Method — Seeking Biological Themes through Pathway-Level Consistency. PLoS ONE 3(9): e3288. doi:10.1371/journa