Oncopression：附有匹配正常组织的癌症基因表达总揽。

Oncopression: gene expression compendium for cancer with matched normal tissues.

机构信息

Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Korea.

Cellex Life Sciences Inc, Daejeon 34141, Korea.

出版信息

Bioinformatics. 2017 Jul 1;33(13):2068-2070. doi: 10.1093/bioinformatics/btx121.

DOI:10.1093/bioinformatics/btx121

PMID:28881874

Abstract

MOTIVATION

Expression profile of normal tissue is primary source to find genes showing aberrant expression pattern specific in matched cancer tissue, but sample number of normal control in public gene expression repositories is disproportionally small compared to cancer and scattered in several datasets.

RESULTS

We built oncopression by integrating several datasets into one large dataset for comprehensive analysis about 25 types of human cancers including 20 640 cancer samples and 6801 normal control profiles. Expression profiles in cancers can be directly compared to normal tissue counterparts. Validity of the integration was tested using immunohistochemical staining results and principal component analysis. We have utilized the pre-release version of oncopression to identify cancer-specific genes in several studies.

AVAILABILITY AND IMPLEMENTATION

Free access at http://www.oncopression.com and all expression data are available for download at the site.

CONTACTS

cchoi@kaist.ac.kr or jungsullee@gmail.com.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

动机

正常组织的表达谱是发现特定于匹配癌症组织的异常表达模式的基因的主要来源，但与癌症相比，公共基因表达数据库中正常对照的样本数量不成比例地较少，而且分散在几个数据集。

结果

我们通过将多个数据集整合到一个大型数据集中，构建了 oncopression，用于对包括 20640 个癌症样本和 6801 个正常对照谱在内的 25 种人类癌症进行综合分析。癌症中的表达谱可以直接与正常组织相对比。我们使用免疫组织化学染色结果和主成分分析来测试集成的有效性。我们已经在几项研究中利用 oncopression 的预发布版本来识别癌症特异性基因。