bc-GenExMiner: an easy-to-use online platform for gene prognostic analyses in breast cancer
bc-GenExMiner: an easy-to-use online platform for gene prognostic analyses in breast cancer
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DOI：
10.1007/s10549-011-1457-7
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发表时间：
2012-02-01
影响因子：
3.8
通讯作者：
Campion, Loic
中科院分区：
文献类型：
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作者：
Jezequel, Pascal;Campone, Mario;Campion, Loic
基因预后荟萃分析应受益于乳腺肿瘤基因组数据在过去十年中获得的。目的是开发一个用户友好的，基于网络的应用程序，基于DNA微阵列的结果，称为“乳腺癌基因表达矿工”（bc-GenExMiner），以提高基因预后分析性能，通过使用相同的生物信息学过程。bc-GenExMiner是作为一个基于Web的工具开发的，包括MySQL关系数据库。使用R统计软件和软件包进行生存分析。分子分型进行了三个单样本预测（SSP）和三个亚型聚类模型（SCM）。已纳入21个公共数据集。在3,414名康复的乳腺癌患者中，1,209人经历了轻蔑事件。通过三种SSP和三种SCM对3，063例患者进行了分子亚型分型。此外，建立了稳定亚型患者的三个稳健列表，以最大限度地提高分子分配的可靠性。基因预后分析通过单变量考克斯比例风险模型进行，并且可以对按淋巴结（N）、雌激素受体（ER）或分子亚型状态划分的群组进行。评估基因相对于诺丁汉预后指数和佐剂的独立预后影响。进行在线调整的考克斯比例风险模型。bc-GenExMiner允许没有特定计算技能的研究人员通过考克斯比例风险模型在大型合并队列上轻松快速地评估基因在乳腺癌中的体内预后作用，这些队列可以根据不同的预后参数进行划分：N，ER和分子亚型。通过分子亚型的预后分析也可以在三种稳健的分子亚型分类中进行。
Gene prognostic meta-analyses should benefit from breast tumour genomic data obtained during the last decade. The aim was to develop a user-friendly, web-based application, based on DNA microarrays results, called "breast cancer Gene-Expression Miner" (bc-GenExMiner) to improve gene prognostic analysis performance by using the same bioinformatics process. bc-GenExMiner was developed as a web-based tool including a MySQL relational database. Survival analyses are performed with R statistical software and packages. Molecular subtyping was performed by means of three single sample predictors (SSPs) and three subtype clustering models (SCMs). Twenty-one public data sets have been included. Among the 3,414 recovered breast cancer patients, 1,209 experienced a pejorative event. Molecular subtyping by means of three SSPs and three SCMs was performed for 3,063 patients. Furthermore, three robust lists of stable subtyped patients were built to maximize reliability of molecular assignment. Gene prognostic analyses are done by means of univariate Cox proportional hazards model and may be conducted on cohorts split by nodal (N), oestrogen receptor (ER), or molecular subtype status. To evaluate independent prognostic impact of genes relative to Nottingham Prognostic Index and Adjuvant! Online, adjusted Cox proportional hazards models are performed. bc-GenExMiner allows researchers without specific computation skills to easily and quickly evaluate the in vivo prognostic role of genes in breast cancer by means of Cox proportional hazards model on large pooled cohorts, which may be split according to different prognostic parameters: N, ER, and molecular subtype. Prognostic analyses by molecular subtype may also be performed in three robust molecular subtype classifications.