Biomarker Benchmark - GSE27854

<b><br>[NOTICE: This data set has been deprecated. Please see our new version of the data (and additional data sets) here: https://osf.io/mhk93 ]</b><br><b><br></b>"Purpose: The purpose of this study is to identify a novel biomarker related with distant metastases of colorectal cancer (CRC).Experimental Design: We investigated mRNA expression profiles in 115 patients with CRC using an Affymetrix Gene Chip, and copy number profiles in 122 patients with CRC using an Affymetrix DNA Sty array. Genes in common between copy number and expression data were extracted as candidate genes. We analyzed the mRNA expression of candidate gene by quantitative reverse transcription polymerase chain reaction (RT-PCR) in 86 patients as a validation study. Furthermore, we analyzed the protein expression of candidate gene by immunohistochemical study in 269 patients, and investigated the relationship between protein expression and clinicopathologic features.<br>Results: By the combination of copy number analysis and gene expression analysis, We extracted 2 candidate genes related with distant metastases of CRC. Several reports show that NUCKS1, one of candidate genes, is overexpressed in several cancer tissues. But a study about the relationship between NUCKS1 and CRC is none. The mRNA expression of NUCKS1 in cancer tissues was significantly higher than those in normal tissues. Overexpression of NUCKS1 protein was associated with significantly worse relapse-free survival of CRC. Overexpression of NUCKS1 protein was an independent risk factor for recurrence of CRC.<br>Conclusion: The overexpression of NUCKS1 would be a new biomarker predicting recurrence after colorectal surgery."<br>http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27854<br>We have included gene-expression data, the outcome (class) being predicted, and any clinical covariates. When gene-expression data were processed in multiple batches, we have provided batch information. Each data set is organized into a file set, where each contains all pertinent files for an individual dataset. The gene expression files have been normalized using both the SCAN and UPC methods using the SCAN.UPC package in Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html). We summarized the data at the gene level using the BrainArray resource (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/20.0.0/ensg.asp). We used Ensembl identifiers. The class, clinical, and batch data were hand curated to ensure consistency ("tidy data" formatting). In addition, the data files have been formatted to be imported easily into the ML-Flex machine learning package (http://mlflex.sourceforge.net/).

<b><br>[注意：本数据集已弃用。请访问以下链接获取新版数据集（及其他新增数据集）：https://osf.io/mhk93 ]</b><br><b><br></b>研究目的：本研究旨在筛选与结直肠癌（colorectal cancer, CRC）远处转移相关的新型生物标志物。实验设计：本研究采用Affymetrix基因芯片检测115例CRC患者的mRNA表达谱，同时采用Affymetrix DNA Sty芯片检测122例CRC患者的拷贝数谱。提取拷贝数数据与表达数据的交集基因作为候选基因。随后，选取86例患者的样本，通过定量逆转录聚合酶链反应（quantitative reverse transcription polymerase chain reaction, RT-PCR）验证候选基因的mRNA表达水平，作为验证队列；此外，选取269例患者的样本，通过免疫组化研究检测候选基因的蛋白表达水平，并分析蛋白表达与临床病理特征之间的关联。研究结果：通过联合拷贝数分析与基因表达分析，本研究共筛选出2个与CRC远处转移相关的候选基因。已有多项研究表明，候选基因之一NUCKS1在多种癌组织中呈高表达，但目前尚无关于NUCKS1与CRC关联的相关研究。CRC癌组织中NUCKS1的mRNA表达水平显著高于正常组织。NUCKS1蛋白高表达与CRC患者更差的无复发生存期显著相关，且NUCKS1蛋白高表达是CRC患者术后复发的独立危险因素。研究结论：NUCKS1高表达可作为结直肠癌术后复发预测的新型生物标志物。http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27854本数据集包含基因表达数据、待预测的结局（分类标签）及所有临床协变量。若基因表达数据经多批次处理，本数据集亦提供批次信息。每个数据集均以文件集形式组织，每个文件集包含单个数据集的全部相关文件。基因表达文件已通过Bioconductor中的SCAN.UPC软件包，采用SCAN与UPC两种方法进行标准化处理（https://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html）。本研究采用BrainArray数据库资源（http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/20.0.0/ensg.asp）在基因水平对数据进行汇总，并使用Ensembl标识符进行基因标注。分类标签、临床数据及批次数据均经过人工整理以确保一致性，采用“整洁数据（tidy data）”格式。此外，本数据集文件已优化，可直接导入ML-Flex机器学习软件包（http://mlflex.sourceforge.net/）。