人结肠癌第二代 RNA 测序数据的计算生物学研究流程

王文渊;江华;潘海霞;杨浩;彭谨;周志远

肿瘤代谢与营养电子杂志 ›› 2016, Vol. 3 ›› Issue (3) : 178-183.

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肿瘤代谢与营养电子杂志 ›› 2016, Vol. 3 ›› Issue (3) : 178-183. DOI: 10.16689/j.cnki.cn11-9349/r.2016.03.013
论著

人结肠癌第二代 RNA 测序数据的计算生物学研究流程

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The computation biology analysis protocol of next-generation high-throughput RNA-sequencing data from human colon cancer

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摘要

摘要:目的 以人结肠癌 RNA 测序数据分析为例,介绍新一代高通量中的 RNA 测序(RNA-sequencingRNA-seq
技术在转录组与基因表达谱方面的应用。 方法  基于 Linux 平台的开源分析软件和人结肠癌 RNA 测序数据,建立完整的
RNA-seq 测序数据处理和分析流程,并对其中的软件选择、质量控制、下游分析进行讨论。 结果  基于现有主流的 RNA-seq
计算生物学分析技术,建立起了一套免费开源的 RNA 测序计算生物学处理和分析流程,并从中鉴定出了数个在结肠癌表
达中存在显著差异的基因。 结论  这项研究为 RNA-seq 数据清理、计算建模和分析提供了具有良好操作性的方案。作为一
个临床肿瘤 RNA-seq 
研究范本,以供从事于类似研究的临床科研工作者参考。

Abstract

Abstract: Objective To introduce an application of the next-generation high-throughput RNA-sequencing (RNA-seq) technology on transcriptomes and gene expression profiles research, based on the RNA-seq data from human colon cancer. Methods Based on the open-source analysis software of Linux platform and RNA-seq data from human colon cancer tissue, the complete workflow of RNA-seq data processing and analysis protocol would be established. And the software selection, quality control and downstream analysis in this workflow would be discussed. Results By using the mainstream RNA-seq computation biology techniques, a set of free and open-source RNA-seq data processing and analysis computational biology protocol have been established. And there were several difference-expressed genes were identified from this human colon cancer RNA-seq data analysis workflow. Conclusions This study provided an easy-to-use protocol for RNA-seq data clean, computation modeling and analysis. As an example of clinical oncology research, it could be referenced for the clinical investigators working on similar study.

关键词

结肠癌 / RNA 测序 / 下一代测序技术 / 转录组 / 计算生物学

Key words

Colon cancer / RNA sequencing / Next-generation sequencing / Transcriptomes / Computation biology

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王文渊;江华;潘海霞;杨浩;彭谨;周志远. 人结肠癌第二代 RNA 测序数据的计算生物学研究流程[J]. 肿瘤代谢与营养电子杂志. 2016, 3(3): 178-183 https://doi.org/10.16689/j.cnki.cn11-9349/r.2016.03.013
WANG Wen-yuan;JIANG Hua;PAN Hai-xia;YANG Hao;PENG Jin;ZHOU Zhi-yuan. The computation biology analysis protocol of next-generation high-throughput RNA-sequencing data from human colon cancer[J]. Electronic Journal of Metabolism and Nutrition of Cancer. 2016, 3(3): 178-183 https://doi.org/10.16689/j.cnki.cn11-9349/r.2016.03.013

基金

四川省科技厅项目(2011SZ0336,2012SZ0181 和 2015SZ0110)

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