Close
Help




JOURNAL

Cancer Informatics

Disease Biomarker Query from RNA-Seq Data

Submit a Paper


Cancer Informatics 2014:Suppl. 1 81-94

Review

Published on 14 Oct 2014

DOI: 10.4137/CIN.S13876


Further metadata provided in PDF



Sign up for email alerts to receive notifications of new articles published in Cancer Informatics

Abstract

As a revolutionary way to unveil transcription, RNA-Seq technologies are challenging bioinformatics for its large data volumes and complexities. A large number of computational models have been proposed for differential expression (DE) analysis and normalization from different standing points. However, there were no studies available yet to conduct disease biomarker discovery for this type of high-resolution digital gene expression data, which will actually be essential to explore its potential in clinical bioinformatics. Although there were many biomarker discovery algorithms available in traditional omics communities, they cannot be applied to RNA-Seq count data to seek biomarkers directly for its special characteristics. In this work, we have presented a biomarker discovery algorithm, SEQ-Marker for RNA-Seq data, which is built on a novel data-driven feature selection algorithm, nonnegative singular value approximation (NSVA), which contributes to the robustness and sensitivity of the following DE analysis by taking advantages of the built-in characteristics of RNA-Seq count data. As a biomarker discovery algorithm built on network marker topology, the proposed SEQ-Marker not only bridges transcriptomics and systems biology but also contributes to clinical diagnostics.



Downloads

PDF  (2.30 MB PDF FORMAT)

RIS citation   (ENDNOTE, REFERENCE MANAGER, PROCITE, REFWORKS)

BibTex citation   (BIBDESK, LATEX)

XML

PMC HTML


Sharing


What Your Colleagues Say About Cancer Informatics
Cancer Informatics has become an increasingly important source for research in the methodology of cancer genomics and the novel use of informatics technology. I have been impressed by the journal's contents and have been very gratified by the number of accesses to my recent publication. Cancer Informatics has filled an important gap in cancer research journals.
Dr Richard Simon (Chief, Biometric Research Branch, National Cancer Institute, USA )
More Testimonials

Quick Links


New article and journal news notification services
Email Alerts RSS Feeds
Facebook Google+ Twitter
Pinterest Tumblr YouTube