title: Identifying grade/stage-related active modules in human co-regulatory networks: a case study for breast cancer.
abstract: The histological grade/stage of tumor is widely acknowledged as an important clinical prognostic factor for cancer progression. Recent experimental studies have explored the following two topics at the molecular level: (1) whether or not gene expression levels vary by different degrees among different tumor grades/stages, and (2) whether some well-defined modules could distinguish one grade/stage from another. In this article, using breast cancer as an example, we investigated this topic and identified grade/stage-related active modules under the framework of a weighted network integrated from a human protein interaction network and a transcriptional regulatory network. Our results enabled us to draw the conclusion that the gene expression profile could provide more clues about tumor grade, but reveals less evidence about tumor stage. In addition, we found that our modular biomarker method had additional advantages in identifying some tumor grade/stage-related genes with slightly altered expression. According to our case study, the framework we introduced could be used for other cancers to identify their modules during grading or staging.
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Hei Longjiang Province, China.
authors.forename: Chenchen
authors.initials: C
authors.lastname: Feng
authors.forename: Lina
authors.initials: L
authors.lastname: Chen
authors.forename: Wan
authors.initials: W
authors.lastname: Li
authors.forename: Hong
authors.initials: H
authors.lastname: Wang
authors.forename: Liangcai
authors.initials: L
authors.lastname: Zhang
authors.forename: Xu
authors.initials: X
authors.lastname: Jia
authors.forename: Zhengqiang
authors.initials: Z
authors.lastname: Miao
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Qu
authors.forename: Weiguo
authors.initials: W
authors.lastname: Li
authors.forename: Weiming
authors.initials: W
authors.lastname: He
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology*; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics / Q000502:physiology; D053263:Gene Regulatory Networks / Q000235:genetics*; D006801:Humans; D009367:Neoplasm Staging / Q000379:methods*